12-94471701-C-T

Variant names:

• chr12-94471701-C-T
• rs1520724

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 0.567 in 151,916 control chromosomes in the GnomAD database, including 24,424 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 (24424 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.164
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.61).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.631 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: 0.567 AC: 86012 AN: 151800 Hom.: 24389 Cov.: 31

Gnomad AFR AF: 0.571

Gnomad AMI AF: 0.557

Gnomad AMR AF: 0.566

Gnomad ASJ AF: 0.541

Gnomad EAS AF: 0.649

Gnomad SAS AF: 0.556

Gnomad FIN AF: 0.520

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.567

Gnomad OTH AF: 0.560

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

GnomAD4 genome AF: 0.567 AC: 86099 AN: 151916 Hom.: 24424 Cov.: 31 AF XY: 0.565 AC XY: 41925 AN XY: 74238

African (AFR) AF: 0.571 AC: 23660 AN: 41400

American (AMR) AF: 0.567 AC: 8652 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.541 AC: 1875 AN: 3466

East Asian (EAS) AF: 0.650 AC: 3357 AN: 5168

South Asian (SAS) AF: 0.556 AC: 2678 AN: 4818

European-Finnish (FIN) AF: 0.520 AC: 5481 AN: 10550

Middle Eastern (MID) AF: 0.541 AC: 159 AN: 294

European-Non Finnish (NFE) AF: 0.567 AC: 38552 AN: 67936

Other (OTH) AF: 0.559 AC: 1180 AN: 2112

Alfa AF: 0.568 Hom.: 60178

Bravo AF: 0.571

Asia WGS AF: 0.631 AC: 2194 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	13
DANN	Benign	0.77
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs1520724; hg19: chr12-94865477;