12-57670954-A-C

Variant names:

• chr12-57670954-A-C
• rs10876994

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 0.226 in 152,164 control chromosomes in the GnomAD database, including 5,033 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 0.23 (5033 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.237
• Publications: 27 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.595 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: 0.226 AC: 34401 AN: 152046 Hom.: 5030 Cov.: 33

Gnomad AFR AF: 0.0749

Gnomad AMI AF: 0.303

Gnomad AMR AF: 0.218

Gnomad ASJ AF: 0.244

Gnomad EAS AF: 0.613

Gnomad SAS AF: 0.490

Gnomad FIN AF: 0.341

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.253

Gnomad OTH AF: 0.211

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

GnomAD4 genome AF: 0.226 AC: 34414 AN: 152164 Hom.: 5033 Cov.: 33 AF XY: 0.236 AC XY: 17567 AN XY: 74360

African (AFR) AF: 0.0748 AC: 3105 AN: 41538

American (AMR) AF: 0.219 AC: 3343 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.244 AC: 848 AN: 3472

East Asian (EAS) AF: 0.613 AC: 3169 AN: 5170

South Asian (SAS) AF: 0.491 AC: 2367 AN: 4822

European-Finnish (FIN) AF: 0.341 AC: 3609 AN: 10572

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.253 AC: 17202 AN: 67984

Other (OTH) AF: 0.213 AC: 450 AN: 2112

Alfa AF: 0.219 Hom.: 1883

Bravo AF: 0.208

Asia WGS AF: 0.489 AC: 1698 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	14
DANN	Benign	0.78
PhyloP100		0.24

Splicing

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

Other links and lift over

dbSNP: rs10876994; hg19: chr12-58064737;