rs12991703

Variant names:

• chr2-119062670-G-T
• rs12991703

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 0.481 in 151,806 control chromosomes in the GnomAD database, including 18,107 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 0.48 (18107 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.433

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.505 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: 0.481 AC: 72959 AN: 151686 Hom.: 18083 Cov.: 31

Gnomad AFR AF: 0.511

Gnomad AMI AF: 0.445

Gnomad AMR AF: 0.456

Gnomad ASJ AF: 0.457

Gnomad EAS AF: 0.0588

Gnomad SAS AF: 0.480

Gnomad FIN AF: 0.504

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.498

Gnomad OTH AF: 0.494

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

GnomAD4 genome AF: 0.481 AC: 73032 AN: 151806 Hom.: 18107 Cov.: 31 AF XY: 0.480 AC XY: 35582 AN XY: 74172

Gnomad4 AFR AF: 0.511

Gnomad4 AMR AF: 0.456

Gnomad4 ASJ AF: 0.457

Gnomad4 EAS AF: 0.0587

Gnomad4 SAS AF: 0.482

Gnomad4 FIN AF: 0.504

Gnomad4 NFE AF: 0.498

Gnomad4 OTH AF: 0.492

Alfa AF: 0.494 Hom.: 2501

Bravo AF: 0.475

Asia WGS AF: 0.279 AC: 973 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.6
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12991703; hg19: chr2-119820246; COSMIC: COSV60101295;