rs7294540

Variant names:

• chr12-1790548-A-C
• rs7294540

Your query was ambiguous. Multiple possible variants found:

• chr12-1790548-A-C
• chr12-1790548-A-G
• chr12-1790548-A-T

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 0.431 in 151,860 control chromosomes in the GnomAD database, including 16,657 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 0.43 (16657 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.566 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.431 AC: 65453 AN: 151742 Hom.: 16656 Cov.: 32

Gnomad AFR AF: 0.155

Gnomad AMI AF: 0.629

Gnomad AMR AF: 0.396

Gnomad ASJ AF: 0.591

Gnomad EAS AF: 0.473

Gnomad SAS AF: 0.455

Gnomad FIN AF: 0.561

Gnomad MID AF: 0.544

Gnomad NFE AF: 0.571

Gnomad OTH AF: 0.427

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

GnomAD4 genome AF: 0.431 AC: 65461 AN: 151860 Hom.: 16657 Cov.: 32 AF XY: 0.431 AC XY: 31982 AN XY: 74184

African (AFR) AF: 0.155 AC: 6403 AN: 41396

American (AMR) AF: 0.396 AC: 6053 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.591 AC: 2047 AN: 3466

East Asian (EAS) AF: 0.474 AC: 2440 AN: 5146

South Asian (SAS) AF: 0.454 AC: 2183 AN: 4804

European-Finnish (FIN) AF: 0.561 AC: 5900 AN: 10518

Middle Eastern (MID) AF: 0.554 AC: 163 AN: 294

European-Non Finnish (NFE) AF: 0.571 AC: 38805 AN: 67954

Other (OTH) AF: 0.425 AC: 895 AN: 2104

Alfa AF: 0.520 Hom.: 33869

Bravo AF: 0.407

Asia WGS AF: 0.424 AC: 1478 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.1
DANN	Benign	0.23
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs7294540; hg19: chr12-1899714;