12-73473927-A-G

Variant names:

• chr12-73473927-A-G
• rs1915282

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 0.641 in 152,028 control chromosomes in the GnomAD database, including 31,790 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 0.64 (31790 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.37
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.756 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.641 AC: 97325 AN: 151910 Hom.: 31754 Cov.: 31

Gnomad AFR AF: 0.763

Gnomad AMI AF: 0.586

Gnomad AMR AF: 0.584

Gnomad ASJ AF: 0.552

Gnomad EAS AF: 0.768

Gnomad SAS AF: 0.606

Gnomad FIN AF: 0.531

Gnomad MID AF: 0.608

Gnomad NFE AF: 0.594

Gnomad OTH AF: 0.651

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

GnomAD4 genome AF: 0.641 AC: 97408 AN: 152028 Hom.: 31790 Cov.: 31 AF XY: 0.638 AC XY: 47395 AN XY: 74286

African (AFR) AF: 0.763 AC: 31673 AN: 41498

American (AMR) AF: 0.583 AC: 8901 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.552 AC: 1915 AN: 3468

East Asian (EAS) AF: 0.767 AC: 3954 AN: 5154

South Asian (SAS) AF: 0.608 AC: 2930 AN: 4820

European-Finnish (FIN) AF: 0.531 AC: 5606 AN: 10552

Middle Eastern (MID) AF: 0.599 AC: 176 AN: 294

European-Non Finnish (NFE) AF: 0.594 AC: 40352 AN: 67958

Other (OTH) AF: 0.648 AC: 1368 AN: 2112

Alfa AF: 0.601 Hom.: 14043

Bravo AF: 0.649

Asia WGS AF: 0.694 AC: 2412 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.35
DANN	Benign	0.76
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs1915282; hg19: chr12-73867707;