2-232440673-C-T

Position:

• chr2-232440673-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 0.229 in 151,792 control chromosomes in the GnomAD database, including 4,554 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 0.23 (4554 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.661

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• 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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.229 AC: 34770 AN: 151674 Hom.: 4553 Cov.: 34

Gnomad AFR AF: 0.121

Gnomad AMI AF: 0.428

Gnomad AMR AF: 0.214

Gnomad ASJ AF: 0.357

Gnomad EAS AF: 0.102

Gnomad SAS AF: 0.191

Gnomad FIN AF: 0.260

Gnomad MID AF: 0.315

Gnomad NFE AF: 0.296

Gnomad OTH AF: 0.246

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

GnomAD4 genome AF: 0.229 AC: 34768 AN: 151792 Hom.: 4554 Cov.: 34 AF XY: 0.227 AC XY: 16840 AN XY: 74240

Gnomad4 AFR AF: 0.121

Gnomad4 AMR AF: 0.213

Gnomad4 ASJ AF: 0.357

Gnomad4 EAS AF: 0.102

Gnomad4 SAS AF: 0.192

Gnomad4 FIN AF: 0.260

Gnomad4 NFE AF: 0.296

Gnomad4 OTH AF: 0.245

Alfa AF: 0.134 Hom.: 237

Bravo AF: 0.222

Asia WGS AF: 0.146 AC: 512 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.94
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs35849718; hg19: chr2-233305383;