rs12024204

chr1-79777316-A-G

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.473

Gnomad4 AMR AF: 0.601

Gnomad4 ASJ AF: 0.648

Gnomad4 EAS AF: 0.348

Gnomad4 SAS AF: 0.516

Gnomad4 FIN AF: 0.592

Gnomad4 NFE AF: 0.533

Gnomad4 OTH AF: 0.523

Alfa AF: 0.531 Hom.: 32563

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

Splicing

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

Publications

LitVar

Other links and lift over

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