3-66772733-C-A

Variant names:

• chr3-66772733-C-A
• rs11709625

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 12 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.106 AC: 4419 AN: 41500

American (AMR) AF: 0.150 AC: 2299 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.145 AC: 505 AN: 3472

East Asian (EAS) AF: 0.171 AC: 883 AN: 5168

South Asian (SAS) AF: 0.101 AC: 488 AN: 4810

European-Finnish (FIN) AF: 0.145 AC: 1540 AN: 10596

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.191 AC: 12959 AN: 67984

Other (OTH) AF: 0.138 AC: 291 AN: 2114

Alfa AF: 0.175 Hom.: 8794

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
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs11709625; hg19: chr3-66823157;