rs7911500

chr10-5995763-C-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 0.0787 in 152,246 control chromosomes in the GnomAD database, including 646 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 0.079 (646 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.633

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.114 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: 0.0787 AC: 11979 AN: 152128 Hom.: 646 Cov.: 32

Gnomad AFR AF: 0.0217

Gnomad AMI AF: 0.162

Gnomad AMR AF: 0.0915

Gnomad ASJ AF: 0.164

Gnomad EAS AF: 0.000770

Gnomad SAS AF: 0.0236

Gnomad FIN AF: 0.0636

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.116

Gnomad OTH AF: 0.108

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

GnomAD4 genome AF: 0.0787 AC: 11978 AN: 152246 Hom.: 646 Cov.: 32 AF XY: 0.0751 AC XY: 5587 AN XY: 74442

Gnomad4 AFR AF: 0.0217

Gnomad4 AMR AF: 0.0914

Gnomad4 ASJ AF: 0.164

Gnomad4 EAS AF: 0.000771

Gnomad4 SAS AF: 0.0234

Gnomad4 FIN AF: 0.0636

Gnomad4 NFE AF: 0.116

Gnomad4 OTH AF: 0.107

Alfa AF: 0.113 Hom.: 1505

Bravo AF: 0.0800

Asia WGS AF: 0.0170 AC: 60 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	2.8
Dann	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7911500; hg19: chr10-6037726;