2-88129052-C-T

Position:

• chr2-88129052-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 0.401 in 152,048 control chromosomes in the GnomAD database, including 13,228 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 0.40 (13228 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.359

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.454 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: 0.401 AC: 60960 AN: 151930 Hom.: 13226 Cov.: 32

Gnomad AFR AF: 0.272

Gnomad AMI AF: 0.492

Gnomad AMR AF: 0.448

Gnomad ASJ AF: 0.413

Gnomad EAS AF: 0.204

Gnomad SAS AF: 0.222

Gnomad FIN AF: 0.639

Gnomad MID AF: 0.401

Gnomad NFE AF: 0.459

Gnomad OTH AF: 0.410

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

GnomAD4 genome AF: 0.401 AC: 60975 AN: 152048 Hom.: 13228 Cov.: 32 AF XY: 0.403 AC XY: 29980 AN XY: 74318

Gnomad4 AFR AF: 0.271

Gnomad4 AMR AF: 0.448

Gnomad4 ASJ AF: 0.413

Gnomad4 EAS AF: 0.204

Gnomad4 SAS AF: 0.222

Gnomad4 FIN AF: 0.639

Gnomad4 NFE AF: 0.458

Gnomad4 OTH AF: 0.406

Alfa AF: 0.439 Hom.: 25116

Bravo AF: 0.383

Asia WGS AF: 0.225 AC: 786 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.1
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2919872; hg19: chr2-88428571;