2-29057895-C-T

Position:

• chr2-29057895-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 0.201 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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.672

Genes affected

(HGNC:):

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/exons	MANE	Protein	UniProt
		n.29057895C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;