rs952054

Variant names:

• chr12-42776209-G-A
• rs952054

Your query was ambiguous. Multiple possible variants found:

• chr12-42776209-G-A
• chr12-42776209-G-C
• chr12-42776209-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 0.139 in 152,184 control chromosomes in the GnomAD database, including 2,041 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 0.14 (2041 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0740

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 (EAS) allele frequency at 95% confidence interval = 0.414 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: 0.139 AC: 21140 AN: 152066 Hom.: 2038 Cov.: 32

Gnomad AFR AF: 0.0492

Gnomad AMI AF: 0.149

Gnomad AMR AF: 0.122

Gnomad ASJ AF: 0.100

Gnomad EAS AF: 0.428

Gnomad SAS AF: 0.286

Gnomad FIN AF: 0.265

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.148

Gnomad OTH AF: 0.131

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

GnomAD4 genome AF: 0.139 AC: 21163 AN: 152184 Hom.: 2041 Cov.: 32 AF XY: 0.148 AC XY: 11043 AN XY: 74386

Gnomad4 AFR AF: 0.0492

Gnomad4 AMR AF: 0.122

Gnomad4 ASJ AF: 0.100

Gnomad4 EAS AF: 0.428

Gnomad4 SAS AF: 0.287

Gnomad4 FIN AF: 0.265

Gnomad4 NFE AF: 0.148

Gnomad4 OTH AF: 0.136

Alfa AF: 0.0542 Hom.: 85

Bravo AF: 0.122

Asia WGS AF: 0.366 AC: 1270 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	1.5
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs952054; hg19: chr12-43170011;