rs2288657

Positions:

• chr2-127637923-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 0.0585 in 152,264 control chromosomes in the GnomAD database, including 327 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 0.059 (327 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.135

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.132 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: 0.0583 AC: 8877 AN: 152146 Hom.: 319 Cov.: 33

Gnomad AFR AF: 0.0913

Gnomad AMI AF: 0.0461

Gnomad AMR AF: 0.0409

Gnomad ASJ AF: 0.0484

Gnomad EAS AF: 0.140

Gnomad SAS AF: 0.104

Gnomad FIN AF: 0.00960

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0409

Gnomad OTH AF: 0.0612

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

GnomAD4 genome AF: 0.0585 AC: 8912 AN: 152264 Hom.: 327 Cov.: 33 AF XY: 0.0588 AC XY: 4375 AN XY: 74448

Gnomad4 AFR AF: 0.0917

Gnomad4 AMR AF: 0.0408

Gnomad4 ASJ AF: 0.0484

Gnomad4 EAS AF: 0.140

Gnomad4 SAS AF: 0.105

Gnomad4 FIN AF: 0.00960

Gnomad4 NFE AF: 0.0409

Gnomad4 OTH AF: 0.0643

Alfa AF: 0.0463 Hom.: 223

Bravo AF: 0.0624

Asia WGS AF: 0.122 AC: 425 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	8.1
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2288657; hg19: chr2-128395498;