2-120365807-T-G

Position:

• chr2-120365807-T-G

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 0.687 in 152,176 control chromosomes in the GnomAD database, including 36,632 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 0.69 (36632 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.316

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.82 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: 0.687 AC: 104467 AN: 152056 Hom.: 36599 Cov.: 33

Gnomad AFR AF: 0.827

Gnomad AMI AF: 0.593

Gnomad AMR AF: 0.651

Gnomad ASJ AF: 0.681

Gnomad EAS AF: 0.820

Gnomad SAS AF: 0.601

Gnomad FIN AF: 0.665

Gnomad MID AF: 0.680

Gnomad NFE AF: 0.611

Gnomad OTH AF: 0.677

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

GnomAD4 genome AF: 0.687 AC: 104551 AN: 152176 Hom.: 36632 Cov.: 33 AF XY: 0.690 AC XY: 51309 AN XY: 74386

Gnomad4 AFR AF: 0.827

Gnomad4 AMR AF: 0.651

Gnomad4 ASJ AF: 0.681

Gnomad4 EAS AF: 0.819

Gnomad4 SAS AF: 0.598

Gnomad4 FIN AF: 0.665

Gnomad4 NFE AF: 0.611

Gnomad4 OTH AF: 0.682

Alfa AF: 0.622 Hom.: 47973

Bravo AF: 0.693

Asia WGS AF: 0.738 AC: 2566 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.4
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12711941; hg19: chr2-121123383;