rs12025436

Variant names:

• chr1-79840299-G-A
• rs12025436

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 0.115 in 151,926 control chromosomes in the GnomAD database, including 1,056 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 0.11 (1056 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.129
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.217 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: 0.115 AC: 17427 AN: 151808 Hom.: 1056 Cov.: 32

Gnomad AFR AF: 0.0971

Gnomad AMI AF: 0.223

Gnomad AMR AF: 0.114

Gnomad ASJ AF: 0.124

Gnomad EAS AF: 0.228

Gnomad SAS AF: 0.0968

Gnomad FIN AF: 0.0895

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.120

Gnomad OTH AF: 0.115

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

GnomAD4 genome AF: 0.115 AC: 17423 AN: 151926 Hom.: 1056 Cov.: 32 AF XY: 0.113 AC XY: 8420 AN XY: 74256

African (AFR) AF: 0.0970 AC: 4023 AN: 41482

American (AMR) AF: 0.114 AC: 1743 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.124 AC: 431 AN: 3466

East Asian (EAS) AF: 0.228 AC: 1166 AN: 5122

South Asian (SAS) AF: 0.0963 AC: 464 AN: 4820

European-Finnish (FIN) AF: 0.0895 AC: 948 AN: 10594

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.120 AC: 8164 AN: 67904

Other (OTH) AF: 0.113 AC: 238 AN: 2108

Alfa AF: 0.122 Hom.: 4672

Bravo AF: 0.119

Asia WGS AF: 0.131 AC: 458 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	8.3
DANN	Benign	0.49
PhyloP100		0.13

Splicing

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

Other links and lift over

dbSNP: rs12025436; hg19: chr1-80305984;