2-224042630-C-T

Position:

• chr2-224042630-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 0.444 in 151,928 control chromosomes in the GnomAD database, including 16,979 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 0.44 (16979 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0290

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.55 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.224042630C>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.444 AC: 67421 AN: 151812 Hom.: 16975 Cov.: 32

Gnomad AFR AF: 0.194

Gnomad AMI AF: 0.407

Gnomad AMR AF: 0.519

Gnomad ASJ AF: 0.528

Gnomad EAS AF: 0.301

Gnomad SAS AF: 0.541

Gnomad FIN AF: 0.599

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.555

Gnomad OTH AF: 0.475

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

GnomAD4 genome AF: 0.444 AC: 67433 AN: 151928 Hom.: 16979 Cov.: 32 AF XY: 0.449 AC XY: 33305 AN XY: 74256

Gnomad4 AFR AF: 0.193

Gnomad4 AMR AF: 0.519

Gnomad4 ASJ AF: 0.528

Gnomad4 EAS AF: 0.300

Gnomad4 SAS AF: 0.542

Gnomad4 FIN AF: 0.599

Gnomad4 NFE AF: 0.555

Gnomad4 OTH AF: 0.471

Alfa AF: 0.524 Hom.: 9660

Bravo AF: 0.425

Asia WGS AF: 0.413 AC: 1437 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	12
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs282254; hg19: chr2-224907347;