15-87839033-A-G

Variant names:

• chr15-87839033-A-G
• rs7403703

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.491 in 151,806 control chromosomes in the GnomAD database, including 19,076 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 0.49 (19076 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: No conservation score assigned
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.634 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.491 AC: 74435 AN: 151686 Hom.: 19038 Cov.: 31

Gnomad AFR AF: 0.640

Gnomad AMI AF: 0.457

Gnomad AMR AF: 0.464

Gnomad ASJ AF: 0.407

Gnomad EAS AF: 0.501

Gnomad SAS AF: 0.595

Gnomad FIN AF: 0.384

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.419

Gnomad OTH AF: 0.484

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

GnomAD4 genome AF: 0.491 AC: 74527 AN: 151806 Hom.: 19076 Cov.: 31 AF XY: 0.491 AC XY: 36406 AN XY: 74198

African (AFR) AF: 0.641 AC: 26499 AN: 41368

American (AMR) AF: 0.464 AC: 7067 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.407 AC: 1409 AN: 3462

East Asian (EAS) AF: 0.501 AC: 2586 AN: 5164

South Asian (SAS) AF: 0.596 AC: 2865 AN: 4808

European-Finnish (FIN) AF: 0.384 AC: 4050 AN: 10552

Middle Eastern (MID) AF: 0.500 AC: 147 AN: 294

European-Non Finnish (NFE) AF: 0.419 AC: 28470 AN: 67920

Other (OTH) AF: 0.486 AC: 1018 AN: 2096

Alfa AF: 0.462 Hom.: 2050

Bravo AF: 0.502

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.97
DANN	Benign	0.59

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs7403703; hg19: chr15-88382264; COSMIC: COSV51408112;