12-47944267-C-A

Variant names:

• chr12-47944267-C-A
• rs4237856

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 0.81 in 152,204 control chromosomes in the GnomAD database, including 50,598 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 0.81 (50598 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.424
• Publications: 13 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.61).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.935 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: 0.810 AC: 123228 AN: 152086 Hom.: 50537 Cov.: 32

Gnomad AFR AF: 0.942

Gnomad AMI AF: 0.763

Gnomad AMR AF: 0.836

Gnomad ASJ AF: 0.810

Gnomad EAS AF: 0.792

Gnomad SAS AF: 0.702

Gnomad FIN AF: 0.744

Gnomad MID AF: 0.718

Gnomad NFE AF: 0.745

Gnomad OTH AF: 0.797

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

GnomAD4 genome AF: 0.810 AC: 123348 AN: 152204 Hom.: 50598 Cov.: 32 AF XY: 0.809 AC XY: 60217 AN XY: 74410

African (AFR) AF: 0.942 AC: 39144 AN: 41536

American (AMR) AF: 0.837 AC: 12802 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.810 AC: 2811 AN: 3472

East Asian (EAS) AF: 0.792 AC: 4102 AN: 5178

South Asian (SAS) AF: 0.702 AC: 3389 AN: 4826

European-Finnish (FIN) AF: 0.744 AC: 7879 AN: 10586

Middle Eastern (MID) AF: 0.721 AC: 212 AN: 294

European-Non Finnish (NFE) AF: 0.745 AC: 50631 AN: 67988

Other (OTH) AF: 0.797 AC: 1684 AN: 2112

Alfa AF: 0.769 Hom.: 25126

Bravo AF: 0.825

Asia WGS AF: 0.774 AC: 2690 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.61
CADD	Benign	4.5
DANN	Benign	0.82
PhyloP100		0.42

Splicing

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

Other links and lift over

dbSNP: rs4237856; hg19: chr12-48338050;