chr2-118120458-A-G

Position:

• chr2-118120458-A-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 0.253 in 152,100 control chromosomes in the GnomAD database, including 5,355 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 0.25 (5355 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.737

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.377 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: 0.253 AC: 38432 AN: 151982 Hom.: 5351 Cov.: 32

Gnomad AFR AF: 0.136

Gnomad AMI AF: 0.236

Gnomad AMR AF: 0.311

Gnomad ASJ AF: 0.296

Gnomad EAS AF: 0.391

Gnomad SAS AF: 0.320

Gnomad FIN AF: 0.235

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.297

Gnomad OTH AF: 0.254

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

GnomAD4 genome AF: 0.253 AC: 38453 AN: 152100 Hom.: 5355 Cov.: 32 AF XY: 0.251 AC XY: 18671 AN XY: 74358

Gnomad4 AFR AF: 0.136

Gnomad4 AMR AF: 0.311

Gnomad4 ASJ AF: 0.296

Gnomad4 EAS AF: 0.392

Gnomad4 SAS AF: 0.320

Gnomad4 FIN AF: 0.235

Gnomad4 NFE AF: 0.297

Gnomad4 OTH AF: 0.251

Alfa AF: 0.292 Hom.: 7300

Bravo AF: 0.254

Asia WGS AF: 0.315 AC: 1095 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.088
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13028041; hg19: chr2-118878034;