3-12264088-T-C

Variant names:

• chr3-12264088-T-C
• rs6798713

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 0.187 in 152,066 control chromosomes in the GnomAD database, including 2,804 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 (2804 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.487
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.389 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: 0.187 AC: 28359 AN: 151948 Hom.: 2792 Cov.: 31

Gnomad AFR AF: 0.197

Gnomad AMI AF: 0.107

Gnomad AMR AF: 0.166

Gnomad ASJ AF: 0.120

Gnomad EAS AF: 0.403

Gnomad SAS AF: 0.148

Gnomad FIN AF: 0.150

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.183

Gnomad OTH AF: 0.158

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

GnomAD4 genome AF: 0.187 AC: 28384 AN: 152066 Hom.: 2804 Cov.: 31 AF XY: 0.185 AC XY: 13732 AN XY: 74348

African (AFR) AF: 0.197 AC: 8176 AN: 41504

American (AMR) AF: 0.166 AC: 2529 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.120 AC: 415 AN: 3468

East Asian (EAS) AF: 0.403 AC: 2077 AN: 5152

South Asian (SAS) AF: 0.148 AC: 716 AN: 4824

European-Finnish (FIN) AF: 0.150 AC: 1583 AN: 10574

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.183 AC: 12424 AN: 67948

Other (OTH) AF: 0.158 AC: 334 AN: 2112

Alfa AF: 0.178 Hom.: 1473

Bravo AF: 0.190

Asia WGS AF: 0.218 AC: 759 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	3.6
DANN	Benign	0.62
PhyloP100		-0.49

Splicing

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

Other links and lift over

dbSNP: rs6798713; hg19: chr3-12305587;