12-66187097-C-G

Variant names:

• chr12-66187097-C-G
• rs2701652

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 0.756 in 152,038 control chromosomes in the GnomAD database, including 44,294 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 0.76 (44294 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.78
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.881 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: 0.756 AC: 114870 AN: 151920 Hom.: 44239 Cov.: 31

Gnomad AFR AF: 0.888

Gnomad AMI AF: 0.815

Gnomad AMR AF: 0.622

Gnomad ASJ AF: 0.775

Gnomad EAS AF: 0.884

Gnomad SAS AF: 0.759

Gnomad FIN AF: 0.670

Gnomad MID AF: 0.787

Gnomad NFE AF: 0.708

Gnomad OTH AF: 0.734

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

GnomAD4 genome AF: 0.756 AC: 114981 AN: 152038 Hom.: 44294 Cov.: 31 AF XY: 0.754 AC XY: 56068 AN XY: 74316

African (AFR) AF: 0.888 AC: 36860 AN: 41490

American (AMR) AF: 0.622 AC: 9503 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.775 AC: 2687 AN: 3468

East Asian (EAS) AF: 0.884 AC: 4562 AN: 5162

South Asian (SAS) AF: 0.760 AC: 3660 AN: 4818

European-Finnish (FIN) AF: 0.670 AC: 7071 AN: 10560

Middle Eastern (MID) AF: 0.795 AC: 232 AN: 292

European-Non Finnish (NFE) AF: 0.708 AC: 48119 AN: 67948

Other (OTH) AF: 0.732 AC: 1544 AN: 2108

Alfa AF: 0.720 Hom.: 4995

Bravo AF: 0.756

Asia WGS AF: 0.806 AC: 2804 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.13
DANN	Benign	0.56
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs2701652; hg19: chr12-66580877;