rs2582520

chr14-104845730-T-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: ENST00000556430.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.660

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 (NFE) allele frequency at 95% confidence interval = 0.811 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000556430.1	n.3068T>C		non_coding_transcript_exon_variant	1/1

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;