2-240882989-C-T

Variant names:

• chr2-240882989-C-T
• rs6437372

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 0.586 in 152,048 control chromosomes in the GnomAD database, including 26,405 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 0.59 (26405 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.903
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.602 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: 0.586 AC: 88971 AN: 151930 Hom.: 26375 Cov.: 33

Gnomad AFR AF: 0.581

Gnomad AMI AF: 0.657

Gnomad AMR AF: 0.517

Gnomad ASJ AF: 0.502

Gnomad EAS AF: 0.589

Gnomad SAS AF: 0.397

Gnomad FIN AF: 0.678

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.607

Gnomad OTH AF: 0.577

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

GnomAD4 genome AF: 0.586 AC: 89038 AN: 152048 Hom.: 26405 Cov.: 33 AF XY: 0.582 AC XY: 43217 AN XY: 74306

African (AFR) AF: 0.581 AC: 24088 AN: 41440

American (AMR) AF: 0.516 AC: 7893 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.502 AC: 1741 AN: 3466

East Asian (EAS) AF: 0.588 AC: 3045 AN: 5178

South Asian (SAS) AF: 0.395 AC: 1904 AN: 4818

European-Finnish (FIN) AF: 0.678 AC: 7154 AN: 10548

Middle Eastern (MID) AF: 0.507 AC: 149 AN: 294

European-Non Finnish (NFE) AF: 0.607 AC: 41258 AN: 67994

Other (OTH) AF: 0.573 AC: 1208 AN: 2110

Alfa AF: 0.587 Hom.: 4525

Bravo AF: 0.577

Asia WGS AF: 0.492 AC: 1714 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.95
DANN	Benign	0.22
PhyloP100		-0.90

Splicing

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

Other links and lift over

dbSNP: rs6437372; hg19: chr2-241822406;