rs10510378

chr3-7925254-T-Cchr3-7925254-T-G

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 0.112 in 152,254 control chromosomes in the GnomAD database, including 1,054 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 0.11 (1054 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0280

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.12 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: 0.112 AC: 17016 AN: 152136 Hom.: 1051 Cov.: 32

Gnomad AFR AF: 0.122

Gnomad AMI AF: 0.226

Gnomad AMR AF: 0.0833

Gnomad ASJ AF: 0.0764

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.0540

Gnomad FIN AF: 0.135

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.121

Gnomad OTH AF: 0.118

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

GnomAD4 genome AF: 0.112 AC: 17037 AN: 152254 Hom.: 1054 Cov.: 32 AF XY: 0.109 AC XY: 8079 AN XY: 74450

Gnomad4 AFR AF: 0.122

Gnomad4 AMR AF: 0.0833

Gnomad4 ASJ AF: 0.0764

Gnomad4 EAS AF: 0.000578

Gnomad4 SAS AF: 0.0537

Gnomad4 FIN AF: 0.135

Gnomad4 NFE AF: 0.121

Gnomad4 OTH AF: 0.117

Alfa AF: 0.106 Hom.: 1105

Bravo AF: 0.108

Asia WGS AF: 0.0310 AC: 109 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	1.8
Dann	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10510378; hg19: chr3-7966941;