rs275418

chr2-114030499-C-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 0.0583 in 151,524 control chromosomes in the GnomAD database, including 543 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 0.058 (543 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.389

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.135 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: 0.0581 AC: 8802 AN: 151422 Hom.: 539 Cov.: 31

Gnomad AFR AF: 0.138

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0570

Gnomad ASJ AF: 0.0167

Gnomad EAS AF: 0.136

Gnomad SAS AF: 0.118

Gnomad FIN AF: 0.0119

Gnomad MID AF: 0.0417

Gnomad NFE AF: 0.00986

Gnomad OTH AF: 0.0479

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

GnomAD4 genome AF: 0.0583 AC: 8830 AN: 151524 Hom.: 543 Cov.: 31 AF XY: 0.0596 AC XY: 4410 AN XY: 74016

Gnomad4 AFR AF: 0.138

Gnomad4 AMR AF: 0.0574

Gnomad4 ASJ AF: 0.0167

Gnomad4 EAS AF: 0.136

Gnomad4 SAS AF: 0.118

Gnomad4 FIN AF: 0.0119

Gnomad4 NFE AF: 0.00986

Gnomad4 OTH AF: 0.0480

Alfa AF: 0.0436 Hom.: 62

Bravo AF: 0.0643

Asia WGS AF: 0.135 AC: 470 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
Cadd	Benign	9.5
Dann	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs275418; hg19: chr2-114788076;