rs952054

Positions:

• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;