rs12696304

Variant names:

• chr3-169763483-C-G
• rs12696304

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 0.378 in 152,024 control chromosomes in the GnomAD database, including 12,364 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 0.38 (12364 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.38
• Publications: 131 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.662 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.378 AC: 57407 AN: 151906 Hom.: 12320 Cov.: 32

Gnomad AFR AF: 0.552

Gnomad AMI AF: 0.238

Gnomad AMR AF: 0.410

Gnomad ASJ AF: 0.222

Gnomad EAS AF: 0.681

Gnomad SAS AF: 0.378

Gnomad FIN AF: 0.276

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.268

Gnomad OTH AF: 0.367

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

GnomAD4 genome AF: 0.378 AC: 57502 AN: 152024 Hom.: 12364 Cov.: 32 AF XY: 0.381 AC XY: 28291 AN XY: 74308

African (AFR) AF: 0.552 AC: 22914 AN: 41476

American (AMR) AF: 0.410 AC: 6259 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.222 AC: 767 AN: 3462

East Asian (EAS) AF: 0.681 AC: 3513 AN: 5162

South Asian (SAS) AF: 0.377 AC: 1814 AN: 4812

European-Finnish (FIN) AF: 0.276 AC: 2917 AN: 10552

Middle Eastern (MID) AF: 0.323 AC: 95 AN: 294

European-Non Finnish (NFE) AF: 0.268 AC: 18224 AN: 67974

Other (OTH) AF: 0.371 AC: 782 AN: 2110

Alfa AF: 0.324 Hom.: 1121

Bravo AF: 0.402

Asia WGS AF: 0.527 AC: 1831 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.12
DANN	Benign	0.48
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs12696304; hg19: chr3-169481271;