rs6437372

Positions:

• chr2-240882989-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 0.586 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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.903

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
		n.240882989C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.581

Gnomad4 AMR AF: 0.516

Gnomad4 ASJ AF: 0.502

Gnomad4 EAS AF: 0.588

Gnomad4 SAS AF: 0.395

Gnomad4 FIN AF: 0.678

Gnomad4 NFE AF: 0.607

Gnomad4 OTH AF: 0.573

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6437372; hg19: chr2-241822406;