rs894791

chr12-73519041-G-Achr12-73519041-G-C

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 0.6 in 151,886 control chromosomes in the GnomAD database, including 27,537 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 0.60 (27537 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.724

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.747 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.600 AC: 91045 AN: 151768 Hom.: 27532 Cov.: 31

Gnomad AFR AF: 0.544

Gnomad AMI AF: 0.628

Gnomad AMR AF: 0.577

Gnomad ASJ AF: 0.595

Gnomad EAS AF: 0.767

Gnomad SAS AF: 0.626

Gnomad FIN AF: 0.575

Gnomad MID AF: 0.665

Gnomad NFE AF: 0.627

Gnomad OTH AF: 0.643

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

GnomAD4 genome AF: 0.600 AC: 91086 AN: 151886 Hom.: 27537 Cov.: 31 AF XY: 0.599 AC XY: 44409 AN XY: 74200

Gnomad4 AFR AF: 0.544

Gnomad4 AMR AF: 0.576

Gnomad4 ASJ AF: 0.595

Gnomad4 EAS AF: 0.767

Gnomad4 SAS AF: 0.628

Gnomad4 FIN AF: 0.575

Gnomad4 NFE AF: 0.627

Gnomad4 OTH AF: 0.639

Alfa AF: 0.615 Hom.: 13039

Bravo AF: 0.597

Asia WGS AF: 0.683 AC: 2369 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	0.53
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: rs894791; hg19: chr12-73912821;