chr12-31253973-G-A

Variant names:

• chr12-31253973-G-A
• rs1025624

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 0.33 in 151,298 control chromosomes in the GnomAD database, including 8,291 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 0.33 (8291 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.919
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.482 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.330 AC: 49882 AN: 151178 Hom.: 8278 Cov.: 31

Gnomad AFR AF: 0.487

Gnomad AMI AF: 0.336

Gnomad AMR AF: 0.258

Gnomad ASJ AF: 0.183

Gnomad EAS AF: 0.188

Gnomad SAS AF: 0.120

Gnomad FIN AF: 0.302

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.289

Gnomad OTH AF: 0.292

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

GnomAD4 genome AF: 0.330 AC: 49938 AN: 151298 Hom.: 8291 Cov.: 31 AF XY: 0.326 AC XY: 24070 AN XY: 73922

African (AFR) AF: 0.487 AC: 20070 AN: 41192

American (AMR) AF: 0.258 AC: 3926 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.183 AC: 635 AN: 3466

East Asian (EAS) AF: 0.188 AC: 966 AN: 5128

South Asian (SAS) AF: 0.121 AC: 580 AN: 4808

European-Finnish (FIN) AF: 0.302 AC: 3166 AN: 10486

Middle Eastern (MID) AF: 0.310 AC: 91 AN: 294

European-Non Finnish (NFE) AF: 0.289 AC: 19594 AN: 67696

Other (OTH) AF: 0.289 AC: 606 AN: 2094

Alfa AF: 0.315 Hom.: 613

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.9
DANN	Benign	0.34
PhyloP100		0.92

Splicing

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

Other links and lift over

dbSNP: rs1025624; hg19: chr12-31406907;