rs1025624

Variant names:

• chr12-31253973-G-A
• rs1025624

Your query was ambiguous. Multiple possible variants found:

• chr12-31253973-G-A
• chr12-31253973-G-T

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 0.33 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.330 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

Gnomad4 AFR AF: 0.487

Gnomad4 AMR AF: 0.258

Gnomad4 ASJ AF: 0.183

Gnomad4 EAS AF: 0.188

Gnomad4 SAS AF: 0.121

Gnomad4 FIN AF: 0.302

Gnomad4 NFE AF: 0.289

Gnomad4 OTH AF: 0.289

Alfa AF: 0.315 Hom.: 613

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1025624; hg19: chr12-31406907;