rs894734

Variant names:

• chr12-53925943-A-G
• rs894734

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 0.586 in 152,070 control chromosomes in the GnomAD database, including 27,027 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 0.59 (27027 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.02

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.762 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: 0.586 AC: 89113 AN: 151952 Hom.: 27015 Cov.: 32

Gnomad AFR AF: 0.423

Gnomad AMI AF: 0.591

Gnomad AMR AF: 0.711

Gnomad ASJ AF: 0.585

Gnomad EAS AF: 0.783

Gnomad SAS AF: 0.539

Gnomad FIN AF: 0.610

Gnomad MID AF: 0.541

Gnomad NFE AF: 0.643

Gnomad OTH AF: 0.589

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

GnomAD4 genome AF: 0.586 AC: 89149 AN: 152070 Hom.: 27027 Cov.: 32 AF XY: 0.588 AC XY: 43731 AN XY: 74322

Gnomad4 AFR AF: 0.423

Gnomad4 AMR AF: 0.711

Gnomad4 ASJ AF: 0.585

Gnomad4 EAS AF: 0.783

Gnomad4 SAS AF: 0.540

Gnomad4 FIN AF: 0.610

Gnomad4 NFE AF: 0.643

Gnomad4 OTH AF: 0.587

Alfa AF: 0.631 Hom.: 41995

Bravo AF: 0.593

Asia WGS AF: 0.604 AC: 2099 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	11
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs894734; hg19: chr12-54319727;