2-29057895-C-T

Variant names:

• chr2-29057895-C-T
• rs882632

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 0.201 in 152,104 control chromosomes in the GnomAD database, including 4,166 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 0.20 (4166 hom., cov: 32)
  • Exomes 𝑓: 0.14 (0 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.672

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.293 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: 0.201 AC: 30554 AN: 151972 Hom.: 4167 Cov.: 32

Gnomad AFR AF: 0.0585

Gnomad AMI AF: 0.148

Gnomad AMR AF: 0.180

Gnomad ASJ AF: 0.385

Gnomad EAS AF: 0.00154

Gnomad SAS AF: 0.146

Gnomad FIN AF: 0.231

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.296

Gnomad OTH AF: 0.252

GnomAD4 exome AF: 0.143 AC: 2 AN: 14 Hom.: 0 Cov.: 0 AF XY: 0.200 AC XY: 2 AN XY: 10

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.167

GnomAD4 genome AF: 0.201 AC: 30549 AN: 152090 Hom.: 4166 Cov.: 32 AF XY: 0.196 AC XY: 14567 AN XY: 74318

Gnomad4 AFR AF: 0.0584

Gnomad4 AMR AF: 0.179

Gnomad4 ASJ AF: 0.385

Gnomad4 EAS AF: 0.00154

Gnomad4 SAS AF: 0.147

Gnomad4 FIN AF: 0.231

Gnomad4 NFE AF: 0.296

Gnomad4 OTH AF: 0.250

Alfa AF: 0.232 Hom.: 1555

Bravo AF: 0.191

Asia WGS AF: 0.0650 AC: 226 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.9
DANN	Benign	0.63

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs882632; hg19: chr2-29280761;