rs12562952

chr1-11866999-T-C

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 0.109 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.131

Gnomad4 AMR AF: 0.0840

Gnomad4 ASJ AF: 0.0960

Gnomad4 EAS AF: 0.108

Gnomad4 SAS AF: 0.186

Gnomad4 FIN AF: 0.0535

Gnomad4 NFE AF: 0.105

Gnomad4 OTH AF: 0.109

Alfa AF: 0.106 Hom.: 1308

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12562952; hg19: chr1-11927056;