rs10510971

chr3-68632264-C-A

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 0.083 in 152,042 control chromosomes in the GnomAD database, including 1,323 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 0.083 (1323 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0570

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.235 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: 0.0830 AC: 12604 AN: 151928 Hom.: 1324 Cov.: 32

Gnomad AFR AF: 0.232

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0463

Gnomad ASJ AF: 0.00750

Gnomad EAS AF: 0.247

Gnomad SAS AF: 0.0319

Gnomad FIN AF: 0.0201

Gnomad MID AF: 0.0159

Gnomad NFE AF: 0.00741

Gnomad OTH AF: 0.0579

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

GnomAD4 genome AF: 0.0830 AC: 12625 AN: 152042 Hom.: 1323 Cov.: 32 AF XY: 0.0841 AC XY: 6253 AN XY: 74324

Gnomad4 AFR AF: 0.232

Gnomad4 AMR AF: 0.0463

Gnomad4 ASJ AF: 0.00750

Gnomad4 EAS AF: 0.247

Gnomad4 SAS AF: 0.0317

Gnomad4 FIN AF: 0.0201

Gnomad4 NFE AF: 0.00741

Gnomad4 OTH AF: 0.0568

Alfa AF: 0.0578 Hom.: 93

Bravo AF: 0.0940

Asia WGS AF: 0.123 AC: 427 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
Cadd	Benign	7.7
Dann	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10510971; hg19: chr3-68681415;