dbSNP rs10520361: ENSG00000287544:n.347-56829A>G (chr4-176950734-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000656694.1(ENSG00000287544):n.347-56829A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.171 in 152,102 control chromosomes in the GnomAD database, including 2,993 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 0.17 ( 2993 hom., cov: 32)

Consequence

ENSG00000287544
ENST00000656694.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.22

Publications

2 publications found

Variant links:

Genes affected

ENSG00000287544 (HGNC:):

ENSG00000287544 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=-0.9).

BA1

GnomAd4 highest subpopulation (AFR) 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
ENSG00000287544	ENST00000656694.1 link	n.347-56829A>G		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes

AF:

0.171

AC:

26011

AN:

151984

Hom.:

2974

Cov.:

show subpopulations

Gnomad AFR

AF:

0.329

Gnomad AMI

AF:

0.0603

Gnomad AMR

AF:

0.164

Gnomad ASJ

AF:

0.101

Gnomad EAS

AF:

0.0114

Gnomad SAS

AF:

0.145

Gnomad FIN

AF:

0.106

Gnomad MID

AF:

0.133

Gnomad NFE

AF:

0.107

Gnomad OTH

AF:

0.156

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

GnomAD4 genome

AF:

0.171

AC:

26063

AN:

152102

Hom.:

2993

Cov.:

AF XY:

0.170

AC XY:

12647

AN XY:

74344

show subpopulations

African (AFR)

AF:

0.329

AC:

13637

AN:

41460

American (AMR)

AF:

0.164

AC:

2499

AN:

15278

Ashkenazi Jewish (ASJ)

AF:

0.101

AC:

349

AN:

3468

East Asian (EAS)

AF:

0.0114

AC:

AN:

5176

South Asian (SAS)

AF:

0.145

AC:

698

AN:

4816

European-Finnish (FIN)

AF:

0.106

AC:

1119

AN:

10592

Middle Eastern (MID)

AF:

0.129

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.107

AC:

7282

AN:

67996

Other (OTH)

AF:

0.155

AC:

327

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1035

2070

3106

4141

5176

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

266

532

798

1064

1330

<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:

0.154

Hom.:

306

Bravo

AF:

0.182

Asia WGS

AF:

0.0860

AC:

298

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.57

(source)

DANN

Benign

0.63

PhyloP100

-1.2

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