rs12696090

Variant names:

• chr3-158951899-G-T
• rs12696090

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 0.27 in 152,082 control chromosomes in the GnomAD database, including 6,460 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 0.27 (6460 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.05
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.428 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: 0.270 AC: 40994 AN: 151964 Hom.: 6445 Cov.: 33

Gnomad AFR AF: 0.433

Gnomad AMI AF: 0.306

Gnomad AMR AF: 0.202

Gnomad ASJ AF: 0.312

Gnomad EAS AF: 0.0386

Gnomad SAS AF: 0.115

Gnomad FIN AF: 0.204

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.221

Gnomad OTH AF: 0.282

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

GnomAD4 genome AF: 0.270 AC: 41048 AN: 152082 Hom.: 6460 Cov.: 33 AF XY: 0.265 AC XY: 19725 AN XY: 74352

African (AFR) AF: 0.433 AC: 17965 AN: 41442

American (AMR) AF: 0.201 AC: 3080 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.312 AC: 1083 AN: 3468

East Asian (EAS) AF: 0.0392 AC: 203 AN: 5174

South Asian (SAS) AF: 0.116 AC: 560 AN: 4828

European-Finnish (FIN) AF: 0.204 AC: 2152 AN: 10574

Middle Eastern (MID) AF: 0.340 AC: 100 AN: 294

European-Non Finnish (NFE) AF: 0.221 AC: 15034 AN: 67988

Other (OTH) AF: 0.280 AC: 592 AN: 2116

Alfa AF: 0.236 Hom.: 6476

Bravo AF: 0.280

Asia WGS AF: 0.102 AC: 356 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.8
DANN	Benign	0.57
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs12696090; hg19: chr3-158669688;