rs10507671

Positions:

• chr13-61618498-A-G
• chr13-61618498-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 0.16 in 151,772 control chromosomes in the GnomAD database, including 2,149 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 0.16 (2149 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.887

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.221 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.160 AC: 24279 AN: 151654 Hom.: 2137 Cov.: 32

Gnomad AFR AF: 0.224

Gnomad AMI AF: 0.233

Gnomad AMR AF: 0.114

Gnomad ASJ AF: 0.104

Gnomad EAS AF: 0.202

Gnomad SAS AF: 0.118

Gnomad FIN AF: 0.195

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.128

Gnomad OTH AF: 0.143

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

GnomAD4 genome AF: 0.160 AC: 24318 AN: 151772 Hom.: 2149 Cov.: 32 AF XY: 0.163 AC XY: 12112 AN XY: 74210

Gnomad4 AFR AF: 0.225

Gnomad4 AMR AF: 0.114

Gnomad4 ASJ AF: 0.104

Gnomad4 EAS AF: 0.202

Gnomad4 SAS AF: 0.117

Gnomad4 FIN AF: 0.195

Gnomad4 NFE AF: 0.128

Gnomad4 OTH AF: 0.141

Alfa AF: 0.0714 Hom.: 1174

Bravo AF: 0.158

Asia WGS AF: 0.135 AC: 471 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	7.2
DANN	Benign	0.88

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10507671; hg19: chr13-62192631;