chr3-179321963-A-G

Variant names:

• chr3-179321963-A-G
• rs3806685

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 0.188 in 152,194 control chromosomes in the GnomAD database, including 2,724 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 0.19 (2724 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.32
• Publications: 10 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.237 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: 0.188 AC: 28538 AN: 152074 Hom.: 2723 Cov.: 33

Gnomad AFR AF: 0.182

Gnomad AMI AF: 0.186

Gnomad AMR AF: 0.244

Gnomad ASJ AF: 0.200

Gnomad EAS AF: 0.216

Gnomad SAS AF: 0.207

Gnomad FIN AF: 0.151

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.179

Gnomad OTH AF: 0.210

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

GnomAD4 genome AF: 0.188 AC: 28555 AN: 152194 Hom.: 2724 Cov.: 33 AF XY: 0.191 AC XY: 14227 AN XY: 74412

African (AFR) AF: 0.182 AC: 7544 AN: 41528

American (AMR) AF: 0.243 AC: 3716 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.200 AC: 693 AN: 3472

East Asian (EAS) AF: 0.216 AC: 1120 AN: 5174

South Asian (SAS) AF: 0.207 AC: 997 AN: 4826

European-Finnish (FIN) AF: 0.151 AC: 1606 AN: 10602

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.179 AC: 12205 AN: 68004

Other (OTH) AF: 0.208 AC: 440 AN: 2112

Alfa AF: 0.195 Hom.: 1216

Bravo AF: 0.197

Asia WGS AF: 0.233 AC: 810 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	8.2
DANN	Benign	0.81
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs3806685; hg19: chr3-179039751;