15-85826720-A-T

Variant names:

• chr15-85826720-A-T
• rs10520603

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 0.708 in 151,942 control chromosomes in the GnomAD database, including 39,245 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 0.71 (39245 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0260
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.869 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

Frequencies

GnomAD3 genomes AF: 0.708 AC: 107446 AN: 151824 Hom.: 39200 Cov.: 31

Gnomad AFR AF: 0.877

Gnomad AMI AF: 0.829

Gnomad AMR AF: 0.764

Gnomad ASJ AF: 0.690

Gnomad EAS AF: 0.651

Gnomad SAS AF: 0.711

Gnomad FIN AF: 0.517

Gnomad MID AF: 0.782

Gnomad NFE AF: 0.624

Gnomad OTH AF: 0.721

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

GnomAD4 genome AF: 0.708 AC: 107553 AN: 151942 Hom.: 39245 Cov.: 31 AF XY: 0.703 AC XY: 52199 AN XY: 74262

African (AFR) AF: 0.877 AC: 36340 AN: 41442

American (AMR) AF: 0.764 AC: 11672 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.690 AC: 2392 AN: 3466

East Asian (EAS) AF: 0.651 AC: 3363 AN: 5164

South Asian (SAS) AF: 0.712 AC: 3429 AN: 4814

European-Finnish (FIN) AF: 0.517 AC: 5442 AN: 10528

Middle Eastern (MID) AF: 0.769 AC: 226 AN: 294

European-Non Finnish (NFE) AF: 0.624 AC: 42420 AN: 67950

Other (OTH) AF: 0.720 AC: 1515 AN: 2104

Alfa AF: 0.663 Hom.: 3995

Bravo AF: 0.734

Asia WGS AF: 0.666 AC: 2315 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.1
DANN	Benign	0.58
PhyloP100		-0.026

Splicing

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

Other links and lift over

dbSNP: rs10520603; hg19: chr15-86369951;