rs12024204

Variant names:

• chr1-79777316-A-G
• rs12024204

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 0.523 in 152,020 control chromosomes in the GnomAD database, including 21,033 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 0.52 (21033 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0670
• Publications: 11 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.591 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: 0.523 AC: 79408 AN: 151902 Hom.: 21018 Cov.: 33

Gnomad AFR AF: 0.472

Gnomad AMI AF: 0.426

Gnomad AMR AF: 0.601

Gnomad ASJ AF: 0.648

Gnomad EAS AF: 0.349

Gnomad SAS AF: 0.517

Gnomad FIN AF: 0.592

Gnomad MID AF: 0.582

Gnomad NFE AF: 0.533

Gnomad OTH AF: 0.529

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

GnomAD4 genome AF: 0.523 AC: 79463 AN: 152020 Hom.: 21033 Cov.: 33 AF XY: 0.526 AC XY: 39094 AN XY: 74296

African (AFR) AF: 0.473 AC: 19598 AN: 41464

American (AMR) AF: 0.601 AC: 9180 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.648 AC: 2250 AN: 3470

East Asian (EAS) AF: 0.348 AC: 1800 AN: 5172

South Asian (SAS) AF: 0.516 AC: 2485 AN: 4816

European-Finnish (FIN) AF: 0.592 AC: 6250 AN: 10554

Middle Eastern (MID) AF: 0.575 AC: 169 AN: 294

European-Non Finnish (NFE) AF: 0.533 AC: 36242 AN: 67962

Other (OTH) AF: 0.523 AC: 1101 AN: 2106

Alfa AF: 0.529 Hom.: 47858

Bravo AF: 0.520

Asia WGS AF: 0.425 AC: 1477 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	9.7
DANN	Benign	0.45
PhyloP100		0.067

Splicing

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

Other links and lift over

dbSNP: rs12024204; hg19: chr1-80243001; COSMIC: COSV59960420;