rs2540477

Variant names:

• chr12-96043776-G-A
• rs2540477

Your query was ambiguous. Multiple possible variants found:

• chr12-96043776-G-A
• chr12-96043776-G-C
• chr12-96043776-G-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 0.761 in 152,008 control chromosomes in the GnomAD database, including 44,596 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 0.76 (44596 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.735

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.821 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: 0.761 AC: 115564 AN: 151890 Hom.: 44561 Cov.: 30

Gnomad AFR AF: 0.829

Gnomad AMI AF: 0.748

Gnomad AMR AF: 0.593

Gnomad ASJ AF: 0.741

Gnomad EAS AF: 0.445

Gnomad SAS AF: 0.809

Gnomad FIN AF: 0.817

Gnomad MID AF: 0.764

Gnomad NFE AF: 0.771

Gnomad OTH AF: 0.721

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

GnomAD4 genome AF: 0.761 AC: 115645 AN: 152008 Hom.: 44596 Cov.: 30 AF XY: 0.758 AC XY: 56292 AN XY: 74308

Gnomad4 AFR AF: 0.829

Gnomad4 AMR AF: 0.592

Gnomad4 ASJ AF: 0.741

Gnomad4 EAS AF: 0.446

Gnomad4 SAS AF: 0.808

Gnomad4 FIN AF: 0.817

Gnomad4 NFE AF: 0.771

Gnomad4 OTH AF: 0.722

Alfa AF: 0.756 Hom.: 75609

Bravo AF: 0.741

Asia WGS AF: 0.648 AC: 2256 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.69
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2540477; hg19: chr12-96437554;