chr2-120356687-G-A

Position:

• chr2-120356687-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 0.466 in 146,214 control chromosomes in the GnomAD database, including 15,757 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 0.47 (15757 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.23

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.698 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: 0.466 AC: 68103 AN: 146108 Hom.: 15742 Cov.: 32

Gnomad AFR AF: 0.564

Gnomad AMI AF: 0.437

Gnomad AMR AF: 0.426

Gnomad ASJ AF: 0.371

Gnomad EAS AF: 0.718

Gnomad SAS AF: 0.683

Gnomad FIN AF: 0.435

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.399

Gnomad OTH AF: 0.439

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

GnomAD4 genome AF: 0.466 AC: 68156 AN: 146214 Hom.: 15757 Cov.: 32 AF XY: 0.475 AC XY: 33961 AN XY: 71556

Gnomad4 AFR AF: 0.563

Gnomad4 AMR AF: 0.426

Gnomad4 ASJ AF: 0.371

Gnomad4 EAS AF: 0.718

Gnomad4 SAS AF: 0.683

Gnomad4 FIN AF: 0.435

Gnomad4 NFE AF: 0.399

Gnomad4 OTH AF: 0.445

Alfa AF: 0.412 Hom.: 13534

Bravo AF: 0.443

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.077
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7576183; hg19: chr2-121114263;