rs12452401

Variant names:

• chr17-73692986-A-G
• rs12452401

Your query was ambiguous. Multiple possible variants found:

• chr17-73692986-A-G
• chr17-73692986-A-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 0.513 in 151,888 control chromosomes in the GnomAD database, including 20,054 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 0.51 (20054 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.252

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 (NFE) allele frequency at 95% confidence interval = 0.529 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: 0.513 AC: 77823 AN: 151768 Hom.: 20014 Cov.: 31

Gnomad AFR AF: 0.496

Gnomad AMI AF: 0.475

Gnomad AMR AF: 0.509

Gnomad ASJ AF: 0.449

Gnomad EAS AF: 0.393

Gnomad SAS AF: 0.511

Gnomad FIN AF: 0.535

Gnomad MID AF: 0.452

Gnomad NFE AF: 0.534

Gnomad OTH AF: 0.496

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

GnomAD4 genome AF: 0.513 AC: 77919 AN: 151888 Hom.: 20054 Cov.: 31 AF XY: 0.511 AC XY: 37920 AN XY: 74218

Gnomad4 AFR AF: 0.497

Gnomad4 AMR AF: 0.509

Gnomad4 ASJ AF: 0.449

Gnomad4 EAS AF: 0.393

Gnomad4 SAS AF: 0.512

Gnomad4 FIN AF: 0.535

Gnomad4 NFE AF: 0.534

Gnomad4 OTH AF: 0.495

Alfa AF: 0.527 Hom.: 28029

Bravo AF: 0.507

Asia WGS AF: 0.448 AC: 1555 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	4.8
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: rs12452401; hg19: chr17-71689125;