dbSNP rs705388: ENSG00000304503:n.161-2895T>C (chr2-136549600-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000803876.1(ENSG00000304503):n.161-2895T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.12 in 152,222 control chromosomes in the GnomAD database, including 1,275 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 0.12 ( 1275 hom., cov: 32)

Consequence

ENSG00000304503
ENST00000803876.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.568

Publications

8 publications found

Variant links:

Genes affected

ENSG00000304503 (HGNC:):

ENSG00000304503 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=-0.91).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.204 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105373633	XR_923360.3 link	n.202-2895T>C		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000304503	ENST00000803876.1 link	n.161-2895T>C	intron_variant	Intron 1 of 3
ENSG00000304503	ENST00000803877.1 link	n.158-4696T>C	intron_variant	Intron 1 of 2
ENSG00000304503	ENST00000803878.1 link	n.242-2895T>C	intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.120

AC:

18181

AN:

152104

Hom.:

1277

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0719

Gnomad AMI

AF:

0.0648

Gnomad AMR

AF:

0.139

Gnomad ASJ

AF:

0.309

Gnomad EAS

AF:

0.192

Gnomad SAS

AF:

0.214

Gnomad FIN

AF:

0.110

Gnomad MID

AF:

0.291

Gnomad NFE

AF:

0.122

Gnomad OTH

AF:

0.169

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

GnomAD4 genome

AF:

0.120

AC:

18191

AN:

152222

Hom.:

1275

Cov.:

AF XY:

0.122

AC XY:

9083

AN XY:

74424

show subpopulations

African (AFR)

AF:

0.0719

AC:

2984

AN:

41526

American (AMR)

AF:

0.139

AC:

2125

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.309

AC:

1070

AN:

3466

East Asian (EAS)

AF:

0.192

AC:

995

AN:

5178

South Asian (SAS)

AF:

0.215

AC:

1038

AN:

4822

European-Finnish (FIN)

AF:

0.110

AC:

1164

AN:

10602

Middle Eastern (MID)

AF:

0.296

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.122

AC:

8307

AN:

68018

Other (OTH)

AF:

0.171

AC:

362

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

799

1598

2396

3195

3994

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

206

412

618

824

1030

<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:

0.127

Hom.:

501

Bravo

AF:

0.117

Asia WGS

AF:

0.217

AC:

754

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.43

(source)

DANN

Benign

0.58

PhyloP100

-0.57

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