12-74716021-A-C

Variant names:

• chr12-74716021-A-C
• rs7967572

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 0.57 in 151,982 control chromosomes in the GnomAD database, including 26,377 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 0.57 (26377 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.09).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.756 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: 0.570 AC: 86503 AN: 151864 Hom.: 26326 Cov.: 32

Gnomad AFR AF: 0.763

Gnomad AMI AF: 0.258

Gnomad AMR AF: 0.615

Gnomad ASJ AF: 0.452

Gnomad EAS AF: 0.747

Gnomad SAS AF: 0.624

Gnomad FIN AF: 0.451

Gnomad MID AF: 0.566

Gnomad NFE AF: 0.453

Gnomad OTH AF: 0.551

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

GnomAD4 genome AF: 0.570 AC: 86612 AN: 151982 Hom.: 26377 Cov.: 32 AF XY: 0.572 AC XY: 42456 AN XY: 74266

African (AFR) AF: 0.763 AC: 31658 AN: 41466

American (AMR) AF: 0.616 AC: 9399 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.452 AC: 1569 AN: 3468

East Asian (EAS) AF: 0.747 AC: 3855 AN: 5158

South Asian (SAS) AF: 0.623 AC: 2996 AN: 4810

European-Finnish (FIN) AF: 0.451 AC: 4756 AN: 10538

Middle Eastern (MID) AF: 0.565 AC: 166 AN: 294

European-Non Finnish (NFE) AF: 0.453 AC: 30806 AN: 67956

Other (OTH) AF: 0.555 AC: 1172 AN: 2112

Alfa AF: 0.452 Hom.: 2156

Bravo AF: 0.591

Asia WGS AF: 0.677 AC: 2356 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.81
DANN	Benign	0.31
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs7967572; hg19: chr12-75109801;