rs2582520

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

Genes affected

ENSG00000258811 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000556430.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000258811	ENST00000556430.1	TSL:6	n.3068T>C		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000294960	ENST00000727045.1		n.120-3994A>G		intron	N/A

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 1.00 AC: 8 AN: 8

Middle Eastern (MID) AF: 0.500 AC: 1 AN: 2

European-Non Finnish (NFE) AF: 0.920 AC: 46 AN: 50

Other (OTH) AF: 0.00 AC: 0 AN: 2

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

African (AFR) AF: 0.394 AC: 16353 AN: 41460

American (AMR) AF: 0.612 AC: 9343 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.861 AC: 2991 AN: 3472

East Asian (EAS) AF: 0.342 AC: 1760 AN: 5140

South Asian (SAS) AF: 0.647 AC: 3118 AN: 4822

European-Finnish (FIN) AF: 0.751 AC: 7927 AN: 10556

Middle Eastern (MID) AF: 0.847 AC: 249 AN: 294

European-Non Finnish (NFE) AF: 0.816 AC: 55482 AN: 67970

Other (OTH) AF: 0.702 AC: 1483 AN: 2114

Alfa AF: 0.725 Hom.: 13920

Bravo AF: 0.635

Asia WGS AF: 0.468 AC: 1631 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.2
DANN	Benign	0.72
PhyloP100		-0.66

Splicing

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

Other links and lift over

dbSNP: rs2582520; hg19: chr14-105312067;