2-119062670-G-T

Position:

• chr2-119062670-G-T

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;