12-667205-G-A

Variant names:

• chr12-667205-G-A
• rs7297967

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 0.564 in 152,042 control chromosomes in the GnomAD database, including 24,238 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 0.56 (24238 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.301
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.566 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: 0.564 AC: 85706 AN: 151924 Hom.: 24205 Cov.: 33

Gnomad AFR AF: 0.572

Gnomad AMI AF: 0.408

Gnomad AMR AF: 0.543

Gnomad ASJ AF: 0.544

Gnomad EAS AF: 0.544

Gnomad SAS AF: 0.561

Gnomad FIN AF: 0.654

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.556

Gnomad OTH AF: 0.545

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

GnomAD4 genome AF: 0.564 AC: 85785 AN: 152042 Hom.: 24238 Cov.: 33 AF XY: 0.568 AC XY: 42206 AN XY: 74338

African (AFR) AF: 0.572 AC: 23702 AN: 41454

American (AMR) AF: 0.543 AC: 8281 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.544 AC: 1885 AN: 3468

East Asian (EAS) AF: 0.544 AC: 2814 AN: 5170

South Asian (SAS) AF: 0.560 AC: 2696 AN: 4818

European-Finnish (FIN) AF: 0.654 AC: 6917 AN: 10578

Middle Eastern (MID) AF: 0.439 AC: 129 AN: 294

European-Non Finnish (NFE) AF: 0.557 AC: 37832 AN: 67976

Other (OTH) AF: 0.549 AC: 1158 AN: 2110

Alfa AF: 0.556 Hom.: 4724

Bravo AF: 0.557

Asia WGS AF: 0.596 AC: 2071 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.67
DANN	Benign	0.42
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs7297967; hg19: chr12-776371;