rs11709625

Positions:

• chr3-66772733-C-A
• chr3-66772733-C-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 0.154 in 152,134 control chromosomes in the GnomAD database, including 2,005 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 0.15 (2005 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.110

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.188 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: 0.154 AC: 23462 AN: 152016 Hom.: 2005 Cov.: 32

Gnomad AFR AF: 0.106

Gnomad AMI AF: 0.0738

Gnomad AMR AF: 0.150

Gnomad ASJ AF: 0.145

Gnomad EAS AF: 0.171

Gnomad SAS AF: 0.102

Gnomad FIN AF: 0.145

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.191

Gnomad OTH AF: 0.137

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

GnomAD4 genome AF: 0.154 AC: 23474 AN: 152134 Hom.: 2005 Cov.: 32 AF XY: 0.152 AC XY: 11297 AN XY: 74392

Gnomad4 AFR AF: 0.106

Gnomad4 AMR AF: 0.150

Gnomad4 ASJ AF: 0.145

Gnomad4 EAS AF: 0.171

Gnomad4 SAS AF: 0.101

Gnomad4 FIN AF: 0.145

Gnomad4 NFE AF: 0.191

Gnomad4 OTH AF: 0.138

Alfa AF: 0.174 Hom.: 3789

Bravo AF: 0.153

Asia WGS AF: 0.129 AC: 447 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	7.4
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11709625; hg19: chr3-66823157;