2-232440673-C-T

Variant names:

• chr2-232440673-C-T
• rs35849718

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 0.229 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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.121 AC: 5033 AN: 41532

American (AMR) AF: 0.213 AC: 3256 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.357 AC: 1224 AN: 3430

East Asian (EAS) AF: 0.102 AC: 529 AN: 5184

South Asian (SAS) AF: 0.192 AC: 923 AN: 4810

European-Finnish (FIN) AF: 0.260 AC: 2753 AN: 10572

Middle Eastern (MID) AF: 0.322 AC: 94 AN: 292

European-Non Finnish (NFE) AF: 0.296 AC: 20053 AN: 67684

Other (OTH) AF: 0.245 AC: 514 AN: 2102

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
PhyloP100		-0.66

Splicing

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

Other links and lift over

dbSNP: rs35849718; hg19: chr2-233305383;