rs275418

Variant names:

• chr2-114030499-C-T
• rs275418

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;