chr15-23861661-G-A

Variant names:

• chr15-23861661-G-A
• rs10519445

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 0.432 in 151,990 control chromosomes in the GnomAD database, including 15,902 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 0.43 (15902 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.558
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.528 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: 0.432 AC: 65600 AN: 151872 Hom.: 15895 Cov.: 32

Gnomad AFR AF: 0.195

Gnomad AMI AF: 0.594

Gnomad AMR AF: 0.508

Gnomad ASJ AF: 0.372

Gnomad EAS AF: 0.475

Gnomad SAS AF: 0.536

Gnomad FIN AF: 0.539

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.532

Gnomad OTH AF: 0.454

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

GnomAD4 genome AF: 0.432 AC: 65625 AN: 151990 Hom.: 15902 Cov.: 32 AF XY: 0.436 AC XY: 32386 AN XY: 74286

African (AFR) AF: 0.195 AC: 8076 AN: 41490

American (AMR) AF: 0.508 AC: 7760 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.372 AC: 1291 AN: 3466

East Asian (EAS) AF: 0.475 AC: 2445 AN: 5144

South Asian (SAS) AF: 0.535 AC: 2576 AN: 4812

European-Finnish (FIN) AF: 0.539 AC: 5682 AN: 10548

Middle Eastern (MID) AF: 0.401 AC: 118 AN: 294

European-Non Finnish (NFE) AF: 0.532 AC: 36167 AN: 67948

Other (OTH) AF: 0.460 AC: 968 AN: 2106

Alfa AF: 0.491 Hom.: 55524

Bravo AF: 0.420

Asia WGS AF: 0.524 AC: 1823 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.83
DANN	Benign	0.64
PhyloP100		-0.56

Splicing

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

Other links and lift over

dbSNP: rs10519445; hg19: chr15-24106808;