dbSNP rs1031261: TTC27:c.537+44G>C (chr2-32640454-G-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_017735.5(TTC27):c.537+44G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.139 in 1,592,104 control chromosomes in the GnomAD database, including 18,220 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.14 ( 1615 hom., cov: 32)

Exomes 𝑓: 0.14 ( 16605 hom. )

Consequence

TTC27
NM_017735.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0570

Publications

12 publications found

Variant links:

Genes affected

TTC27 (HGNC:25986): (tetratricopeptide repeat domain 27)

TTC27 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.84).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.329 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TTC27	NM_017735.5 link	c.537+44G>C		intron_variant	Intron 4 of 19	ENST00000317907.9	NP_060205.3	Q6P3X3

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
TTC27	ENST00000317907.9 link	c.537+44G>C	intron_variant	Intron 4 of 19	1	NM_017735.5	ENSP00000313953.4	Q6P3X3
TTC27	ENST00000454690.1 link	n.88+12074G>C	intron_variant	Intron 1 of 3	3		ENSP00000392883.1	F8WCH1
TTC27	ENST00000647819.1 link	n.537+44G>C	intron_variant	Intron 4 of 21			ENSP00000497009.1	A0A3B3IS02
TTC27	ENST00000448773.5 link	c.*86G>C	downstream_gene_variant		4		ENSP00000393327.1	C9JVS4

Frequencies

GnomAD3 genomes

AF:

0.136

AC:

20639

AN:

151936

Hom.:

1612

Cov.:

show subpopulations

Gnomad AFR

AF:

0.117

Gnomad AMI

AF:

0.0648

Gnomad AMR

AF:

0.126

Gnomad ASJ

AF:

0.0965

Gnomad EAS

AF:

0.295

Gnomad SAS

AF:

0.344

Gnomad FIN

AF:

0.158

Gnomad MID

AF:

0.123

Gnomad NFE

AF:

0.122

Gnomad OTH

AF:

0.125

GnomAD2 exomes

AF:

0.173

AC:

41598

AN:

240546

AF XY:

0.181

show subpopulations

Gnomad AFR exome

AF:

0.115

Gnomad AMR exome

AF:

0.159

Gnomad ASJ exome

AF:

0.0974

Gnomad EAS exome

AF:

0.306

Gnomad FIN exome

AF:

0.157

Gnomad NFE exome

AF:

0.129

Gnomad OTH exome

AF:

0.152

GnomAD4 exome

AF:

0.139

AC:

200085

AN:

1440050

Hom.:

16605

Cov.:

AF XY:

0.145

AC XY:

103950

AN XY:

716314

show subpopulations

African (AFR)

AF:

0.118

AC:

3910

AN:

33106

American (AMR)

AF:

0.153

AC:

6677

AN:

43544

Ashkenazi Jewish (ASJ)

AF:

0.0965

AC:

2476

AN:

25648

East Asian (EAS)

AF:

0.278

AC:

10963

AN:

39478

South Asian (SAS)

AF:

0.335

AC:

28204

AN:

84106

European-Finnish (FIN)

AF:

0.152

AC:

7553

AN:

49694

Middle Eastern (MID)

AF:

0.116

AC:

661

AN:

5702

European-Non Finnish (NFE)

AF:

0.119

AC:

131055

AN:

1099090

Other (OTH)

AF:

0.144

AC:

8586

AN:

59682

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.473

Heterozygous variant carriers

7160

14319

21479

28638

35798

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

4862

9724

14586

19448

24310

<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:

0.136

AC:

20660

AN:

152054

Hom.:

1615

Cov.:

AF XY:

0.140

AC XY:

10410

AN XY:

74334

show subpopulations

African (AFR)

AF:

0.118

AC:

4877

AN:

41488

American (AMR)

AF:

0.126

AC:

1919

AN:

15274

Ashkenazi Jewish (ASJ)

AF:

0.0965

AC:

334

AN:

3462

East Asian (EAS)

AF:

0.295

AC:

1527

AN:

5174

South Asian (SAS)

AF:

0.343

AC:

1647

AN:

4798

European-Finnish (FIN)

AF:

0.158

AC:

1662

AN:

10550

Middle Eastern (MID)

AF:

0.119

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.123

AC:

8330

AN:

67988

Other (OTH)

AF:

0.128

AC:

270

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

900

1799

2699

3598

4498

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

250

500

750

1000

1250

<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:

0.132

Hom.:

937

Bravo

AF:

0.131

Asia WGS

AF:

0.333

AC:

1155

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

7.3

(source)

DANN

Benign

0.70

PhyloP100

0.057

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over