chr2-118112002-G-T

Position:

• chr2-118112002-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 0.0455 in 152,110 control chromosomes in the GnomAD database, including 232 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 0.045 (232 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.848

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.143 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: 0.0455 AC: 6917 AN: 151992 Hom.: 232 Cov.: 32

Gnomad AFR AF: 0.0100

Gnomad AMI AF: 0.0724

Gnomad AMR AF: 0.0535

Gnomad ASJ AF: 0.0386

Gnomad EAS AF: 0.152

Gnomad SAS AF: 0.123

Gnomad FIN AF: 0.0779

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0468

Gnomad OTH AF: 0.0383

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

GnomAD4 genome AF: 0.0455 AC: 6920 AN: 152110 Hom.: 232 Cov.: 32 AF XY: 0.0490 AC XY: 3643 AN XY: 74360

Gnomad4 AFR AF: 0.0100

Gnomad4 AMR AF: 0.0535

Gnomad4 ASJ AF: 0.0386

Gnomad4 EAS AF: 0.152

Gnomad4 SAS AF: 0.124

Gnomad4 FIN AF: 0.0779

Gnomad4 NFE AF: 0.0467

Gnomad4 OTH AF: 0.0412

Alfa AF: 0.0435 Hom.: 146

Bravo AF: 0.0405

Asia WGS AF: 0.132 AC: 459 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.4
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12623648; hg19: chr2-118869578;