dbSNP rs7575840: ENSG00000287956:n.240-837C>A (chr2-21050618-G-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000821616.1(ENSG00000287956):n.240-837C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.258 in 152,108 control chromosomes in the GnomAD database, including 5,539 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 0.26 ( 5539 hom., cov: 32)

Consequence

ENSG00000287956
ENST00000821616.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.779

Publications

39 publications found

Variant links:

Genes affected

ENSG00000287956 (HGNC:):

ENSG00000287956 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=-0.92).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.324 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
ENSG00000287956	ENST00000821616.1 link	n.240-837C>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.258

AC:

39251

AN:

151990

Hom.:

5536

Cov.:

show subpopulations

Gnomad AFR

AF:

0.152

Gnomad AMI

AF:

0.351

Gnomad AMR

AF:

0.302

Gnomad ASJ

AF:

0.239

Gnomad EAS

AF:

0.123

Gnomad SAS

AF:

0.141

Gnomad FIN

AF:

0.293

Gnomad MID

AF:

0.127

Gnomad NFE

AF:

0.328

Gnomad OTH

AF:

0.230

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

GnomAD4 genome

AF:

0.258

AC:

39266

AN:

152108

Hom.:

5539

Cov.:

AF XY:

0.255

AC XY:

18939

AN XY:

74364

show subpopulations

African (AFR)

AF:

0.151

AC:

6285

AN:

41512

American (AMR)

AF:

0.302

AC:

4615

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.239

AC:

830

AN:

3472

East Asian (EAS)

AF:

0.123

AC:

638

AN:

5176

South Asian (SAS)

AF:

0.141

AC:

681

AN:

4824

European-Finnish (FIN)

AF:

0.293

AC:

3103

AN:

10578

Middle Eastern (MID)

AF:

0.126

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.328

AC:

22275

AN:

67954

Other (OTH)

AF:

0.229

AC:

483

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1501

3002

4504

6005

7506

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

404

808

1212

1616

2020

<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:

0.291

Hom.:

10044

Bravo

AF:

0.257

Asia WGS

AF:

0.143

AC:

499

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.21

(source)

DANN

Benign

0.32

PhyloP100

-0.78

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