2-2368409-T-C

Position:

• chr2-2368409-T-C

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 0.482 in 151,946 control chromosomes in the GnomAD database, including 17,995 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 0.48 (17995 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.701

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.705 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.2368409T>C		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.481 AC: 73073 AN: 151828 Hom.: 17946 Cov.: 31

Gnomad AFR AF: 0.454

Gnomad AMI AF: 0.206

Gnomad AMR AF: 0.535

Gnomad ASJ AF: 0.391

Gnomad EAS AF: 0.725

Gnomad SAS AF: 0.692

Gnomad FIN AF: 0.583

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.446

Gnomad OTH AF: 0.456

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

GnomAD4 genome AF: 0.482 AC: 73183 AN: 151946 Hom.: 17995 Cov.: 31 AF XY: 0.493 AC XY: 36603 AN XY: 74260

Gnomad4 AFR AF: 0.455

Gnomad4 AMR AF: 0.536

Gnomad4 ASJ AF: 0.391

Gnomad4 EAS AF: 0.724

Gnomad4 SAS AF: 0.691

Gnomad4 FIN AF: 0.583

Gnomad4 NFE AF: 0.446

Gnomad4 OTH AF: 0.464

Alfa AF: 0.453 Hom.: 36019

Bravo AF: 0.474

Asia WGS AF: 0.717 AC: 2490 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.6
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6759198; hg19: chr2-2372181;