2-29057895-C-T

Variant names:

• chr2-29057895-C-T
• rs882632

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 13 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.167 AC: 2 AN: 12

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.0584 AC: 2423 AN: 41510

American (AMR) AF: 0.179 AC: 2738 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.385 AC: 1336 AN: 3472

East Asian (EAS) AF: 0.00154 AC: 8 AN: 5180

South Asian (SAS) AF: 0.147 AC: 708 AN: 4822

European-Finnish (FIN) AF: 0.231 AC: 2430 AN: 10540

Middle Eastern (MID) AF: 0.357 AC: 105 AN: 294

European-Non Finnish (NFE) AF: 0.296 AC: 20139 AN: 67974

Other (OTH) AF: 0.250 AC: 527 AN: 2110

Alfa AF: 0.204 Hom.: 3435

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
PhyloP100		-0.67
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs882632; hg19: chr2-29280761;