15-85826720-A-T

Position:

• chr15-85826720-A-T

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.877

Gnomad4 AMR AF: 0.764

Gnomad4 ASJ AF: 0.690

Gnomad4 EAS AF: 0.651

Gnomad4 SAS AF: 0.712

Gnomad4 FIN AF: 0.517

Gnomad4 NFE AF: 0.624

Gnomad4 OTH AF: 0.720

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10520603; hg19: chr15-86369951;