dbSNP rs6430612: ENSG00000308974:n.120+2103C>T (chr2-136248628-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 ENST00000837573.1(ENSG00000308974):n.120+2103C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.43 in 151,898 control chromosomes in the GnomAD database, including 16,452 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 0.43 ( 16452 hom., cov: 31)

Consequence

ENSG00000308974
ENST00000837573.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.18

Publications

15 publications found

Variant links:

Genes affected

ENSG00000308974 (HGNC:):

ENSG00000308974 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=-0.75).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.565 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000308974	ENST00000837573.1 link	n.120+2103C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.430

AC:

65237

AN:

151780

Hom.:

16455

Cov.:

show subpopulations

Gnomad AFR

AF:

0.306

Gnomad AMI

AF:

0.570

Gnomad AMR

AF:

0.267

Gnomad ASJ

AF:

0.182

Gnomad EAS

AF:

0.0530

Gnomad SAS

AF:

0.242

Gnomad FIN

AF:

0.619

Gnomad MID

AF:

0.124

Gnomad NFE

AF:

0.570

Gnomad OTH

AF:

0.320

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

GnomAD4 genome

AF:

0.430

AC:

65249

AN:

151898

Hom.:

16452

Cov.:

AF XY:

0.419

AC XY:

31116

AN XY:

74240

show subpopulations

African (AFR)

AF:

0.306

AC:

12683

AN:

41416

American (AMR)

AF:

0.267

AC:

4076

AN:

15274

Ashkenazi Jewish (ASJ)

AF:

0.182

AC:

632

AN:

3470

East Asian (EAS)

AF:

0.0528

AC:

273

AN:

5174

South Asian (SAS)

AF:

0.242

AC:

1164

AN:

4814

European-Finnish (FIN)

AF:

0.619

AC:

6500

AN:

10508

Middle Eastern (MID)

AF:

0.127

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.570

AC:

38699

AN:

67932

Other (OTH)

AF:

0.316

AC:

665

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1654

3309

4963

6618

8272

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

592

1184

1776

2368

2960

<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:

0.474

Hom.:

45920

Bravo

AF:

0.397

Asia WGS

AF:

0.162

AC:

565

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.75

CADD

Benign

0.17

(source)

DANN

Benign

0.72

PhyloP100

-2.2

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