NM_000371.4:c.337-18G>C

Variant names:

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_000371.4(TTR):c.337-18G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.045 in 1,612,924 control chromosomes in the GnomAD database, including 2,162 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.060 ( 370 hom., cov: 32)

Exomes 𝑓: 0.043 ( 1792 hom. )

Consequence

TTR
NM_000371.4 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:14

Conservation

PhyloP100: -0.503

Publications

10 publications found

Variant links:

Genes affected

TTR (HGNC:12405): (transthyretin) This gene encodes one of the three prealbumins, which include alpha-1-antitrypsin, transthyretin and orosomucoid. The encoded protein, transthyretin, is a homo-tetrameric carrier protein, which transports thyroid hormones in the plasma and cerebrospinal fluid. It is also involved in the transport of retinol (vitamin A) in the plasma by associating with retinol-binding protein. The protein may also be involved in other intracellular processes including proteolysis, nerve regeneration, autophagy and glucose homeostasis. Mutations in this gene are associated with amyloid deposition, predominantly affecting peripheral nerves or the heart, while a small percentage of the gene mutations are non-amyloidogenic. The mutations are implicated in the etiology of several diseases, including amyloidotic polyneuropathy, euthyroid hyperthyroxinaemia, amyloidotic vitreous opacities, cardiomyopathy, oculoleptomeningeal amyloidosis, meningocerebrovascular amyloidosis and carpal tunnel syndrome. [provided by RefSeq, Aug 2017]

TTR Gene-Disease associations (from GenCC):

amyloidosis, hereditary systemic 1
Inheritance: AD Classification: DEFINITIVE Submitted by: G2P
familial amyloid neuropathy
Inheritance: AD Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Orphanet, Ambry Genetics, Labcorp Genetics (formerly Invitae)
hereditary ATTR amyloidosis
Inheritance: AD Classification: DEFINITIVE Submitted by: ClinGen
heart conduction disease
Inheritance: AD Classification: STRONG Submitted by: Genomics England PanelApp
ATTRV122I amyloidosis
Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

TTR links:

ENSG00000294516 (HGNC:):

ENSG00000294516 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.8).

BP6

Variant 18-31598550-G-C is Benign according to our data. Variant chr18-31598550-G-C is described in ClinVar as Benign. ClinVar VariationId is 36892.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.1 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000371.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TTR	NM_000371.4	MANE Select	c.337-18G>C		intron	N/A	NP_000362.1	P02766

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
TTR	ENST00000237014.8	TSL:1 MANE Select	c.337-18G>C	intron	N/A	ENSP00000237014.4	P02766
TTR	ENST00000649620.1		c.337-18G>C	intron	N/A	ENSP00000497927.1	P02766
TTR	ENST00000858988.1		c.337-18G>C	intron	N/A	ENSP00000529047.1

Frequencies

GnomAD3 genomes

AF:

0.0604

AC:

9168

AN:

151788

Hom.:

367

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0952

Gnomad AMI

AF:

0.0515

Gnomad AMR

AF:

0.104

Gnomad ASJ

AF:

0.0499

Gnomad EAS

AF:

0.0720

Gnomad SAS

AF:

0.0222

Gnomad FIN

AF:

0.0171

Gnomad MID

AF:

0.0665

Gnomad NFE

AF:

0.0389

Gnomad OTH

AF:

0.0581

GnomAD2 exomes

AF:

0.0572

AC:

14357

AN:

250802

AF XY:

0.0507

show subpopulations

Gnomad AFR exome

AF:

0.0969

Gnomad AMR exome

AF:

0.155

Gnomad ASJ exome

AF:

0.0551

Gnomad EAS exome

AF:

0.0740

Gnomad FIN exome

AF:

0.0194

Gnomad NFE exome

AF:

0.0366

Gnomad OTH exome

AF:

0.0477

GnomAD4 exome

AF:

0.0434

AC:

63455

AN:

1461026

Hom.:

1792

Cov.:

AF XY:

0.0421

AC XY:

30588

AN XY:

726838

show subpopulations

African (AFR)

AF:

0.0984

AC:

3271

AN:

33234

American (AMR)

AF:

0.149

AC:

6667

AN:

44676

Ashkenazi Jewish (ASJ)

AF:

0.0525

AC:

1371

AN:

26134

East Asian (EAS)

AF:

0.0608

AC:

2413

AN:

39694

South Asian (SAS)

AF:

0.0198

AC:

1710

AN:

86244

European-Finnish (FIN)

AF:

0.0196

AC:

1045

AN:

53330

Middle Eastern (MID)

AF:

0.0429

AC:

247

AN:

5758

European-Non Finnish (NFE)

AF:

0.0396

AC:

44010

AN:

1111658

Other (OTH)

AF:

0.0451

AC:

2721

AN:

60298

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.496

Heterozygous variant carriers

3314

6628

9941

13255

16569

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

1808

3616

5424

7232

9040

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0604

AC:

9175

AN:

151898

Hom.:

370

Cov.:

AF XY:

0.0590

AC XY:

4384

AN XY:

74268

show subpopulations

African (AFR)

AF:

0.0949

AC:

3916

AN:

41260

American (AMR)

AF:

0.104

AC:

1592

AN:

15250

Ashkenazi Jewish (ASJ)

AF:

0.0499

AC:

173

AN:

3470

East Asian (EAS)

AF:

0.0722

AC:

373

AN:

5168

South Asian (SAS)

AF:

0.0222

AC:

107

AN:

4820

European-Finnish (FIN)

AF:

0.0171

AC:

182

AN:

10620

Middle Eastern (MID)

AF:

0.0646

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0389

AC:

2645

AN:

67998

Other (OTH)

AF:

0.0575

AC:

121

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

429

859

1288

1718

2147

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

100

200

300

400

500

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0201

Hom.:

Bravo

AF:

0.0706

ClinVar

ClinVar submissions

Significance:Benign

Revision:criteria provided, multiple submitters, no conflicts

View on ClinVar

Pathogenic

VUS

Benign

Condition

not specified (6)

not provided (3)

Cardiomyopathy (2)

Amyloidosis, hereditary systemic 1 (1)

Cardiovascular phenotype (1)

Charcot-Marie-Tooth disease (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

0.29

(source)

DANN

Benign

0.59

PhyloP100

-0.50

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over