2-119142357-G-A

Position:

• chr2-119142357-G-A

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 0.483 in 151,904 control chromosomes in the GnomAD database, including 18,584 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 (18584 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.128

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 (NFE) allele frequency at 95% confidence interval = 0.565 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.483 AC: 73264 AN: 151786 Hom.: 18579 Cov.: 32

Gnomad AFR AF: 0.365

Gnomad AMI AF: 0.360

Gnomad AMR AF: 0.521

Gnomad ASJ AF: 0.528

Gnomad EAS AF: 0.139

Gnomad SAS AF: 0.465

Gnomad FIN AF: 0.501

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.570

Gnomad OTH AF: 0.475

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

GnomAD4 genome AF: 0.483 AC: 73296 AN: 151904 Hom.: 18584 Cov.: 32 AF XY: 0.478 AC XY: 35498 AN XY: 74222

Gnomad4 AFR AF: 0.364

Gnomad4 AMR AF: 0.522

Gnomad4 ASJ AF: 0.528

Gnomad4 EAS AF: 0.138

Gnomad4 SAS AF: 0.466

Gnomad4 FIN AF: 0.501

Gnomad4 NFE AF: 0.570

Gnomad4 OTH AF: 0.473

Alfa AF: 0.545 Hom.: 24215

Bravo AF: 0.474

Asia WGS AF: 0.304 AC: 1060 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	3.6
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10205049; hg19: chr2-119899933; COSMIC: COSV60101441;