rs2042484

Variant names:

• chr2-207498338-C-T
• rs2042484
• ENST00000412387.5:n.260+19282G>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000412387.5(ENSG00000223725):​n.260+19282G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.414 in 152,030 control chromosomes in the GnomAD database, including 13,715 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 0.41 (13715 hom., cov: 32)
• Consequence: ENSG00000223725 ENST00000412387.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.217

Genes affected

ENSG00000223725 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.701 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
ENSG00000223725	ENST00000412387.5	n.260+19282G>A		intron_variant	Intron 3 of 4	4
ENSG00000223725	ENST00000418850.1	n.256+19282G>A		intron_variant	Intron 3 of 5	5

Frequencies

GnomAD3 genomes AF: 0.415 AC: 62974 AN: 151910 Hom.: 13722 Cov.: 32

Gnomad AFR AF: 0.337

Gnomad AMI AF: 0.438

Gnomad AMR AF: 0.362

Gnomad ASJ AF: 0.497

Gnomad EAS AF: 0.721

Gnomad SAS AF: 0.497

Gnomad FIN AF: 0.468

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.430

Gnomad OTH AF: 0.456

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

GnomAD4 genome AF: 0.414 AC: 62975 AN: 152030 Hom.: 13715 Cov.: 32 AF XY: 0.418 AC XY: 31047 AN XY: 74298

Gnomad4 AFR AF: 0.337

Gnomad4 AMR AF: 0.362

Gnomad4 ASJ AF: 0.497

Gnomad4 EAS AF: 0.721

Gnomad4 SAS AF: 0.498

Gnomad4 FIN AF: 0.468

Gnomad4 NFE AF: 0.430

Gnomad4 OTH AF: 0.450

Alfa AF: 0.434 Hom.: 29131

Bravo AF: 0.402

Asia WGS AF: 0.551 AC: 1914 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	9.3
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2042484; hg19: chr2-208363062;