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. The variant received -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
• Publications: 2 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 (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

African (AFR) AF: 0.0492 AC: 2045 AN: 41556

American (AMR) AF: 0.122 AC: 1870 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.100 AC: 348 AN: 3470

East Asian (EAS) AF: 0.428 AC: 2215 AN: 5170

South Asian (SAS) AF: 0.287 AC: 1381 AN: 4818

European-Finnish (FIN) AF: 0.265 AC: 2798 AN: 10556

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.148 AC: 10056 AN: 68006

Other (OTH) AF: 0.136 AC: 288 AN: 2114

Alfa AF: 0.0548 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
PhyloP100		-0.074

Splicing

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

Other links and lift over

dbSNP: rs952054; hg19: chr12-43170011;