rs12040131

Variant names:

• chr1-22663205-C-G
• rs12040131

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 0.162 in 152,234 control chromosomes in the GnomAD database, including 2,485 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 0.16 (2485 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.114

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.222 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: 0.162 AC: 24716 AN: 152116 Hom.: 2487 Cov.: 32

Gnomad AFR AF: 0.0511

Gnomad AMI AF: 0.125

Gnomad AMR AF: 0.229

Gnomad ASJ AF: 0.155

Gnomad EAS AF: 0.0250

Gnomad SAS AF: 0.119

Gnomad FIN AF: 0.195

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.225

Gnomad OTH AF: 0.179

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

GnomAD4 genome AF: 0.162 AC: 24713 AN: 152234 Hom.: 2485 Cov.: 32 AF XY: 0.161 AC XY: 11991 AN XY: 74434

Gnomad4 AFR AF: 0.0509

Gnomad4 AMR AF: 0.228

Gnomad4 ASJ AF: 0.155

Gnomad4 EAS AF: 0.0251

Gnomad4 SAS AF: 0.119

Gnomad4 FIN AF: 0.195

Gnomad4 NFE AF: 0.224

Gnomad4 OTH AF: 0.180

Alfa AF: 0.188 Hom.: 421

Bravo AF: 0.163

Asia WGS AF: 0.0840 AC: 293 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.4
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12040131; hg19: chr1-22989698;