12-73519041-G-A

Variant names:

• chr12-73519041-G-A
• rs894791

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 0.6 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
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	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

African (AFR) AF: 0.544 AC: 22520 AN: 41394

American (AMR) AF: 0.576 AC: 8789 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.595 AC: 2064 AN: 3466

East Asian (EAS) AF: 0.767 AC: 3945 AN: 5144

South Asian (SAS) AF: 0.628 AC: 3024 AN: 4816

European-Finnish (FIN) AF: 0.575 AC: 6064 AN: 10550

Middle Eastern (MID) AF: 0.650 AC: 191 AN: 294

European-Non Finnish (NFE) AF: 0.627 AC: 42571 AN: 67942

Other (OTH) AF: 0.639 AC: 1348 AN: 2110

Alfa AF: 0.615 Hom.: 14530

Bravo AF: 0.597

Asia WGS AF: 0.683 AC: 2369 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.53
DANN	Benign	0.34
PhyloP100		-0.72

Splicing

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

Other links and lift over

dbSNP: rs894791; hg19: chr12-73912821;