rs10515869

Positions:

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

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 0.569 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

ACMG classification

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.631

Gnomad4 AMR AF: 0.562

Gnomad4 ASJ AF: 0.496

Gnomad4 EAS AF: 0.558

Gnomad4 SAS AF: 0.454

Gnomad4 FIN AF: 0.480

Gnomad4 NFE AF: 0.562

Gnomad4 OTH AF: 0.560

Alfa AF: 0.561 Hom.: 14254

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10515869; hg19: chr5-163512226;