rs12696090

Variant names:

• chr3-158951899-G-T
• rs12696090

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 0.27 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.270 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

Gnomad4 AFR AF: 0.433

Gnomad4 AMR AF: 0.201

Gnomad4 ASJ AF: 0.312

Gnomad4 EAS AF: 0.0392

Gnomad4 SAS AF: 0.116

Gnomad4 FIN AF: 0.204

Gnomad4 NFE AF: 0.221

Gnomad4 OTH AF: 0.280

Alfa AF: 0.235 Hom.: 5478

Bravo AF: 0.280

Asia WGS AF: 0.102 AC: 356 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12696090; hg19: chr3-158669688;