rs10851470

Variant names:

• chr15-48678083-G-A
• rs10851470

Your query was ambiguous. Multiple possible variants found:

• chr15-48678083-G-A
• chr15-48678083-G-T

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 0.694 in 152,172 control chromosomes in the GnomAD database, including 37,931 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 0.69 (37931 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.103
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.863 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: 0.695 AC: 105606 AN: 152054 Hom.: 37925 Cov.: 32

Gnomad AFR AF: 0.500

Gnomad AMI AF: 0.493

Gnomad AMR AF: 0.759

Gnomad ASJ AF: 0.794

Gnomad EAS AF: 0.885

Gnomad SAS AF: 0.873

Gnomad FIN AF: 0.761

Gnomad MID AF: 0.772

Gnomad NFE AF: 0.757

Gnomad OTH AF: 0.728

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

GnomAD4 genome AF: 0.694 AC: 105640 AN: 152172 Hom.: 37931 Cov.: 32 AF XY: 0.700 AC XY: 52084 AN XY: 74400

African (AFR) AF: 0.499 AC: 20695 AN: 41476

American (AMR) AF: 0.759 AC: 11612 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.794 AC: 2755 AN: 3468

East Asian (EAS) AF: 0.885 AC: 4578 AN: 5174

South Asian (SAS) AF: 0.874 AC: 4217 AN: 4826

European-Finnish (FIN) AF: 0.761 AC: 8081 AN: 10616

Middle Eastern (MID) AF: 0.762 AC: 224 AN: 294

European-Non Finnish (NFE) AF: 0.757 AC: 51485 AN: 67996

Other (OTH) AF: 0.730 AC: 1544 AN: 2114

Alfa AF: 0.735 Hom.: 110179

Bravo AF: 0.684

Asia WGS AF: 0.828 AC: 2877 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.84
DANN	Benign	0.53
PhyloP100		0.10

Splicing

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

Other links and lift over

dbSNP: rs10851470; hg19: chr15-48970280;