Genetic Variant ENST00000674320.1:n.462+1631C>T (chr13-41565109-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000674320.1(ENSG00000288598):n.462+1631C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.13 in 152,166 control chromosomes in the GnomAD database, including 1,647 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 0.13 ( 1647 hom., cov: 33)

Consequence

ENSG00000288598
ENST00000674320.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.331

Publications

17 publications found

Variant links:

Genes affected

ENSG00000288598 (HGNC:):

ENSG00000288598 links:

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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=-0.86).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.233 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000288598	ENST00000674320.1 link	n.462+1631C>T	intron_variant	Intron 4 of 4
ENSG00000288598	ENST00000674416.1 link	n.1720+1631C>T	intron_variant	Intron 3 of 5
ENSG00000288598	ENST00000842280.1 link	n.588+6270C>T	intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes

AF:

0.130

AC:

19812

AN:

152046

Hom.:

1641

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0428

Gnomad AMI

AF:

0.209

Gnomad AMR

AF:

0.238

Gnomad ASJ

AF:

0.151

Gnomad EAS

AF:

0.228

Gnomad SAS

AF:

0.246

Gnomad FIN

AF:

0.186

Gnomad MID

AF:

0.175

Gnomad NFE

AF:

0.133

Gnomad OTH

AF:

0.141

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.130

AC:

19840

AN:

152166

Hom.:

1647

Cov.:

AF XY:

0.137

AC XY:

10201

AN XY:

74382

show subpopulations

African (AFR)

AF:

0.0430

AC:

1786

AN:

41546

American (AMR)

AF:

0.239

AC:

3647

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.151

AC:

524

AN:

3470

East Asian (EAS)

AF:

0.227

AC:

1174

AN:

5172

South Asian (SAS)

AF:

0.245

AC:

1180

AN:

4818

European-Finnish (FIN)

AF:

0.186

AC:

1963

AN:

10568

Middle Eastern (MID)

AF:

0.175

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.133

AC:

9019

AN:

67990

Other (OTH)

AF:

0.145

AC:

306

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

860

1720

2581

3441

4301

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

222

444

666

888

1110

<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:

0.133

Hom.:

4617

Bravo

AF:

0.128

Asia WGS

AF:

0.243

AC:

845

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

1.0

(source)

DANN

Benign

0.37

PhyloP100

-0.33

Splicing

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over