rs12086263

Variant names:

• chr1-152791480-A-G
• rs12086263

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 0.155 in 134,804 control chromosomes in the GnomAD database, including 5,756 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 0.15 (5756 hom., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.240
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.63).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.381 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.155 AC: 20828 AN: 134702 Hom.: 5744 Cov.: 22

Gnomad AFR AF: 0.386

Gnomad AMI AF: 0.0787

Gnomad AMR AF: 0.0909

Gnomad ASJ AF: 0.0563

Gnomad EAS AF: 0.0391

Gnomad SAS AF: 0.0954

Gnomad FIN AF: 0.0537

Gnomad MID AF: 0.0735

Gnomad NFE AF: 0.0599

Gnomad OTH AF: 0.123

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

GnomAD4 genome AF: 0.155 AC: 20867 AN: 134804 Hom.: 5756 Cov.: 22 AF XY: 0.152 AC XY: 10039 AN XY: 65844

African (AFR) AF: 0.386 AC: 14506 AN: 37564

American (AMR) AF: 0.0907 AC: 1245 AN: 13732

Ashkenazi Jewish (ASJ) AF: 0.0563 AC: 177 AN: 3144

East Asian (EAS) AF: 0.0390 AC: 201 AN: 5158

South Asian (SAS) AF: 0.0951 AC: 424 AN: 4458

European-Finnish (FIN) AF: 0.0537 AC: 491 AN: 9148

Middle Eastern (MID) AF: 0.0703 AC: 18 AN: 256

European-Non Finnish (NFE) AF: 0.0599 AC: 3520 AN: 58728

Other (OTH) AF: 0.123 AC: 220 AN: 1790

Alfa AF: 0.137 Hom.: 453

Asia WGS AF: 0.0980 AC: 336 AN: 3416

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.63
CADD	Benign	11
DANN	Benign	0.70
PhyloP100		0.24

Splicing

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

Other links and lift over

dbSNP: rs12086263; hg19: chr1-152763956;