2-232394382-C-T

Variant names:

• chr2-232394382-C-T
• rs2344360

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 0.462 in 151,748 control chromosomes in the GnomAD database, including 16,825 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 0.46 (16825 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.165
• Publications: 0 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 (EAS) allele frequency at 95% confidence interval = 0.555 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: 0.462 AC: 70021 AN: 151630 Hom.: 16818 Cov.: 32

Gnomad AFR AF: 0.323

Gnomad AMI AF: 0.338

Gnomad AMR AF: 0.523

Gnomad ASJ AF: 0.492

Gnomad EAS AF: 0.573

Gnomad SAS AF: 0.556

Gnomad FIN AF: 0.566

Gnomad MID AF: 0.510

Gnomad NFE AF: 0.501

Gnomad OTH AF: 0.467

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

GnomAD4 genome AF: 0.462 AC: 70037 AN: 151748 Hom.: 16825 Cov.: 32 AF XY: 0.466 AC XY: 34524 AN XY: 74122

African (AFR) AF: 0.323 AC: 13348 AN: 41358

American (AMR) AF: 0.524 AC: 7993 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.492 AC: 1703 AN: 3464

East Asian (EAS) AF: 0.573 AC: 2955 AN: 5160

South Asian (SAS) AF: 0.555 AC: 2649 AN: 4774

European-Finnish (FIN) AF: 0.566 AC: 5950 AN: 10504

Middle Eastern (MID) AF: 0.503 AC: 146 AN: 290

European-Non Finnish (NFE) AF: 0.501 AC: 34003 AN: 67936

Other (OTH) AF: 0.468 AC: 982 AN: 2100

Alfa AF: 0.359 Hom.: 1008

Bravo AF: 0.453

Asia WGS AF: 0.582 AC: 2019 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.8
DANN	Benign	0.79
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs2344360; hg19: chr2-233259092;