rs4953717

Variant names:

• chr2-43047761-A-G
• rs4953717
• ENST00000716701.1:n.399-10996T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000716701.1(LINC02580):​n.399-10996T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.731 in 152,094 control chromosomes in the GnomAD database, including 40,890 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 0.73 (40890 hom., cov: 33)
• Consequence: LINC02580 ENST00000716701.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.479
• Publications: 2 publications found

Genes affected

LINC02580 (HGNC:53751): (long intergenic non-protein coding RNA 2580)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.749 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000716701.1. 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
	LINC02580	ENST00000716701.1		n.399-10996T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.731 AC: 111070 AN: 151976 Hom.: 40877 Cov.: 33

Gnomad AFR AF: 0.754

Gnomad AMI AF: 0.672

Gnomad AMR AF: 0.709

Gnomad ASJ AF: 0.778

Gnomad EAS AF: 0.413

Gnomad SAS AF: 0.652

Gnomad FIN AF: 0.705

Gnomad MID AF: 0.731

Gnomad NFE AF: 0.755

Gnomad OTH AF: 0.715

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

GnomAD4 genome AF: 0.731 AC: 111135 AN: 152094 Hom.: 40890 Cov.: 33 AF XY: 0.725 AC XY: 53896 AN XY: 74364

African (AFR) AF: 0.753 AC: 31229 AN: 41480

American (AMR) AF: 0.710 AC: 10842 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.778 AC: 2702 AN: 3472

East Asian (EAS) AF: 0.413 AC: 2135 AN: 5164

South Asian (SAS) AF: 0.651 AC: 3140 AN: 4824

European-Finnish (FIN) AF: 0.705 AC: 7456 AN: 10576

Middle Eastern (MID) AF: 0.748 AC: 220 AN: 294

European-Non Finnish (NFE) AF: 0.755 AC: 51294 AN: 67984

Other (OTH) AF: 0.713 AC: 1504 AN: 2110

Alfa AF: 0.746 Hom.: 37762

Bravo AF: 0.731

Asia WGS AF: 0.538 AC: 1871 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.93
DANN	Benign	0.32
PhyloP100		-0.48

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs4953717;

hg19: chr2-43274900;