rs2582520

Variant names:

• chr14-104845730-T-C
• rs2582520
• ENST00000556430.1:n.3068T>C

Variant summary

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

The ENST00000556430.1(ENSG00000258811):​n.3068T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.655 in 152,068 control chromosomes in the GnomAD database, including 35,482 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 0.65 (35457 hom., cov: 32)
  • Exomes 𝑓: 0.89 (25 hom.)
• Consequence: ENSG00000258811 ENST00000556430.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.660

Genes affected

ENSG00000258811 (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 (NFE) allele frequency at 95% confidence interval = 0.811 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
ENSG00000258811	ENST00000556430.1	n.3068T>C		non_coding_transcript_exon_variant	Exon 1 of 1	6

Frequencies

GnomAD3 genomes AF: 0.655 AC: 99525 AN: 151888 Hom.: 35466 Cov.: 32

Gnomad AFR AF: 0.395

Gnomad AMI AF: 0.905

Gnomad AMR AF: 0.613

Gnomad ASJ AF: 0.861

Gnomad EAS AF: 0.343

Gnomad SAS AF: 0.645

Gnomad FIN AF: 0.751

Gnomad MID AF: 0.858

Gnomad NFE AF: 0.816

Gnomad OTH AF: 0.705

GnomAD4 exome AF: 0.887 AC: 55 AN: 62 Hom.: 25 Cov.: 0 AF XY: 0.857 AC XY: 36 AN XY: 42

Gnomad4 FIN exome AF: 1.00

Gnomad4 NFE exome AF: 0.920

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.655 AC: 99531 AN: 152006 Hom.: 35457 Cov.: 32 AF XY: 0.649 AC XY: 48225 AN XY: 74270

Gnomad4 AFR AF: 0.394

Gnomad4 AMR AF: 0.612

Gnomad4 ASJ AF: 0.861

Gnomad4 EAS AF: 0.342

Gnomad4 SAS AF: 0.647

Gnomad4 FIN AF: 0.751

Gnomad4 NFE AF: 0.816

Gnomad4 OTH AF: 0.702

Alfa AF: 0.746 Hom.: 7323

Bravo AF: 0.635

Asia WGS AF: 0.468 AC: 1631 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	4.2
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: rs2582520; hg19: chr14-105312067;