rs10515869

Variant names:

• chr5-164085220-G-A
• rs10515869

Your query was ambiguous. Multiple possible variants found:

• chr5-164085220-G-A
• chr5-164085220-G-C

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 0.569 in 151,876 control chromosomes in the GnomAD database, including 24,807 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 0.57 (24807 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.438
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.6).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.625 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: 0.569 AC: 86381 AN: 151756 Hom.: 24787 Cov.: 31

Gnomad AFR AF: 0.632

Gnomad AMI AF: 0.401

Gnomad AMR AF: 0.561

Gnomad ASJ AF: 0.496

Gnomad EAS AF: 0.558

Gnomad SAS AF: 0.454

Gnomad FIN AF: 0.480

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.562

Gnomad OTH AF: 0.565

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

GnomAD4 genome AF: 0.569 AC: 86447 AN: 151876 Hom.: 24807 Cov.: 31 AF XY: 0.564 AC XY: 41829 AN XY: 74210

African (AFR) AF: 0.631 AC: 26155 AN: 41428

American (AMR) AF: 0.562 AC: 8571 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.496 AC: 1721 AN: 3472

East Asian (EAS) AF: 0.558 AC: 2868 AN: 5140

South Asian (SAS) AF: 0.454 AC: 2188 AN: 4816

European-Finnish (FIN) AF: 0.480 AC: 5063 AN: 10556

Middle Eastern (MID) AF: 0.517 AC: 152 AN: 294

European-Non Finnish (NFE) AF: 0.562 AC: 38189 AN: 67918

Other (OTH) AF: 0.560 AC: 1177 AN: 2100

Alfa AF: 0.564 Hom.: 19122

Bravo AF: 0.575

Asia WGS AF: 0.483 AC: 1677 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.60
CADD	Benign	9.8
DANN	Benign	0.62
PhyloP100		0.44

Splicing

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

Other links and lift over

dbSNP: rs10515869; hg19: chr5-163512226;