rs12566237

Variant names:

• chr1-96720626-A-G
• rs12566237

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 0.33 in 151,968 control chromosomes in the GnomAD database, including 8,478 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 0.33 (8478 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.35
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.424 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.330 AC: 50164 AN: 151850 Hom.: 8465 Cov.: 31

Gnomad AFR AF: 0.308

Gnomad AMI AF: 0.267

Gnomad AMR AF: 0.318

Gnomad ASJ AF: 0.398

Gnomad EAS AF: 0.413

Gnomad SAS AF: 0.441

Gnomad FIN AF: 0.268

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.339

Gnomad OTH AF: 0.350

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

GnomAD4 genome AF: 0.330 AC: 50220 AN: 151968 Hom.: 8478 Cov.: 31 AF XY: 0.328 AC XY: 24360 AN XY: 74254

African (AFR) AF: 0.309 AC: 12784 AN: 41416

American (AMR) AF: 0.318 AC: 4852 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.398 AC: 1380 AN: 3468

East Asian (EAS) AF: 0.414 AC: 2130 AN: 5146

South Asian (SAS) AF: 0.440 AC: 2118 AN: 4816

European-Finnish (FIN) AF: 0.268 AC: 2834 AN: 10570

Middle Eastern (MID) AF: 0.337 AC: 99 AN: 294

European-Non Finnish (NFE) AF: 0.339 AC: 23029 AN: 67966

Other (OTH) AF: 0.357 AC: 752 AN: 2108

Alfa AF: 0.320 Hom.: 1222

Bravo AF: 0.333

Asia WGS AF: 0.473 AC: 1644 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	6.5
DANN	Benign	0.53
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs12566237; hg19: chr1-97186182;