rs10515260

Variant names:

• chr5-97740844-T-C
• rs10515260
• ENST00000715761.1:n.277+70160T>C

Variant summary

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

The ENST00000715761.1(LINC01340):​n.277+70160T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0666 in 151,654 control chromosomes in the GnomAD database, including 677 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 0.067 (677 hom., cov: 32)
• Consequence: LINC01340 ENST00000715761.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.252
• Publications: 7 publications found

Genes affected

LINC01340 (HGNC:50550): (long intergenic non-protein coding RNA 1340)

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 (AFR) allele frequency at 95% confidence interval = 0.155 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
LINC01340	ENST00000715761.1	n.277+70160T>C		intron_variant	Intron 3 of 6
LINC01340	ENST00000746238.1	n.382+70160T>C		intron_variant	Intron 4 of 8
LINC01340	ENST00000746239.1	n.362+70160T>C		intron_variant	Intron 4 of 9

Frequencies

GnomAD3 genomes AF: 0.0666 AC: 10089 AN: 151536 Hom.: 673 Cov.: 32

Gnomad AFR AF: 0.158

Gnomad AMI AF: 0.00336

Gnomad AMR AF: 0.0448

Gnomad ASJ AF: 0.0585

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0106

Gnomad FIN AF: 0.0227

Gnomad MID AF: 0.0737

Gnomad NFE AF: 0.0329

Gnomad OTH AF: 0.0606

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

GnomAD4 genome AF: 0.0666 AC: 10107 AN: 151654 Hom.: 677 Cov.: 32 AF XY: 0.0661 AC XY: 4899 AN XY: 74146

African (AFR) AF: 0.158 AC: 6548 AN: 41392

American (AMR) AF: 0.0447 AC: 681 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.0585 AC: 203 AN: 3472

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5170

South Asian (SAS) AF: 0.0106 AC: 51 AN: 4812

European-Finnish (FIN) AF: 0.0227 AC: 239 AN: 10514

Middle Eastern (MID) AF: 0.0793 AC: 23 AN: 290

European-Non Finnish (NFE) AF: 0.0329 AC: 2231 AN: 67782

Other (OTH) AF: 0.0604 AC: 127 AN: 2102

Alfa AF: 0.0519 Hom.: 854

Bravo AF: 0.0729

Asia WGS AF: 0.0140 AC: 49 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.9
DANN	Benign	0.51
PhyloP100		-0.25

Splicing

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

Other links and lift over

dbSNP: rs10515260; hg19: chr5-97076548;