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. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.431 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

Gnomad4 AFR AF: 0.155

Gnomad4 AMR AF: 0.396

Gnomad4 ASJ AF: 0.591

Gnomad4 EAS AF: 0.474

Gnomad4 SAS AF: 0.454

Gnomad4 FIN AF: 0.561

Gnomad4 NFE AF: 0.571

Gnomad4 OTH AF: 0.425

Alfa AF: 0.535 Hom.: 27154

Bravo AF: 0.407

Asia WGS AF: 0.424 AC: 1478 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7294540; hg19: chr12-1899714;