dbSNP rs2523685: ENSG00000288587:n.63-4644G>C (chr6-31458479-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 ENST00000673857.1(ENSG00000288587):n.63-4644G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.322 in 151,502 control chromosomes in the GnomAD database, including 9,257 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 0.32 ( 9257 hom., cov: 32)

Consequence

ENSG00000288587
ENST00000673857.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.99

Publications

20 publications found

Variant links:

Genes affected

ENSG00000288587 (HGNC:):

ENSG00000288587 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=-1.05).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.483 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
ENSG00000288587	ENST00000673857.1 link	n.63-4644G>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.322

AC:

48741

AN:

151386

Hom.:

9220

Cov.:

show subpopulations

Gnomad AFR

AF:

0.488

Gnomad AMI

AF:

0.234

Gnomad AMR

AF:

0.405

Gnomad ASJ

AF:

0.364

Gnomad EAS

AF:

0.262

Gnomad SAS

AF:

0.309

Gnomad FIN

AF:

0.258

Gnomad MID

AF:

0.382

Gnomad NFE

AF:

0.216

Gnomad OTH

AF:

0.359

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

GnomAD4 genome

AF:

0.322

AC:

48825

AN:

151502

Hom.:

9257

Cov.:

AF XY:

0.325

AC XY:

24048

AN XY:

74048

show subpopulations

African (AFR)

AF:

0.489

AC:

20112

AN:

41162

American (AMR)

AF:

0.405

AC:

6148

AN:

15164

Ashkenazi Jewish (ASJ)

AF:

0.364

AC:

1262

AN:

3466

East Asian (EAS)

AF:

0.262

AC:

1350

AN:

5146

South Asian (SAS)

AF:

0.309

AC:

1488

AN:

4808

European-Finnish (FIN)

AF:

0.258

AC:

2708

AN:

10512

Middle Eastern (MID)

AF:

0.372

AC:

108

AN:

290

European-Non Finnish (NFE)

AF:

0.216

AC:

14676

AN:

67940

Other (OTH)

AF:

0.361

AC:

760

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1584

3168

4751

6335

7919

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

470

940

1410

1880

2350

<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:

0.142

Hom.:

272

Bravo

AF:

0.341

Asia WGS

AF:

0.303

AC:

1046

AN:

3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.1

CADD

Benign

0.17

(source)

DANN

Benign

0.38

PhyloP100

-2.0

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