rs12562952

Variant names:

• chr1-11866999-T-C
• rs12562952

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 0.109 in 152,068 control chromosomes in the GnomAD database, including 950 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 0.11 (950 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.60
• Publications: 15 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.176 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: 0.109 AC: 16493 AN: 151950 Hom.: 942 Cov.: 31

Gnomad AFR AF: 0.130

Gnomad AMI AF: 0.0636

Gnomad AMR AF: 0.0844

Gnomad ASJ AF: 0.0960

Gnomad EAS AF: 0.108

Gnomad SAS AF: 0.186

Gnomad FIN AF: 0.0535

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.105

Gnomad OTH AF: 0.109

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

GnomAD4 genome AF: 0.109 AC: 16536 AN: 152068 Hom.: 950 Cov.: 31 AF XY: 0.108 AC XY: 8031 AN XY: 74320

African (AFR) AF: 0.131 AC: 5431 AN: 41464

American (AMR) AF: 0.0840 AC: 1281 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.0960 AC: 333 AN: 3470

East Asian (EAS) AF: 0.108 AC: 560 AN: 5182

South Asian (SAS) AF: 0.186 AC: 896 AN: 4816

European-Finnish (FIN) AF: 0.0535 AC: 567 AN: 10592

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.105 AC: 7144 AN: 67980

Other (OTH) AF: 0.109 AC: 230 AN: 2108

Alfa AF: 0.108 Hom.: 2960

Bravo AF: 0.108

Asia WGS AF: 0.175 AC: 608 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.59
DANN	Benign	0.21
PhyloP100		-3.6

Splicing

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

Other links and lift over

dbSNP: rs12562952; hg19: chr1-11927056;