12-6734681-A-G

Variant names:

• chr12-6734681-A-G
• rs2365567

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 0.718 in 151,904 control chromosomes in the GnomAD database, including 39,272 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 0.72 (39272 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.241
• Publications: 13 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.846 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.718 AC: 108924 AN: 151786 Hom.: 39242 Cov.: 30

Gnomad AFR AF: 0.749

Gnomad AMI AF: 0.709

Gnomad AMR AF: 0.760

Gnomad ASJ AF: 0.750

Gnomad EAS AF: 0.765

Gnomad SAS AF: 0.869

Gnomad FIN AF: 0.697

Gnomad MID AF: 0.839

Gnomad NFE AF: 0.676

Gnomad OTH AF: 0.721

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

GnomAD4 genome AF: 0.718 AC: 109001 AN: 151904 Hom.: 39272 Cov.: 30 AF XY: 0.721 AC XY: 53532 AN XY: 74236

African (AFR) AF: 0.749 AC: 30999 AN: 41414

American (AMR) AF: 0.760 AC: 11595 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.750 AC: 2602 AN: 3468

East Asian (EAS) AF: 0.765 AC: 3942 AN: 5152

South Asian (SAS) AF: 0.868 AC: 4180 AN: 4818

European-Finnish (FIN) AF: 0.697 AC: 7349 AN: 10546

Middle Eastern (MID) AF: 0.840 AC: 247 AN: 294

European-Non Finnish (NFE) AF: 0.676 AC: 45935 AN: 67942

Other (OTH) AF: 0.715 AC: 1507 AN: 2108

Alfa AF: 0.687 Hom.: 30855

Bravo AF: 0.720

Asia WGS AF: 0.753 AC: 2618 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.6
DANN	Benign	0.49
PhyloP100		-0.24

Splicing

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

Other links and lift over

dbSNP: rs2365567; hg19: chr12-6843847;