rs10495803

Variant names:

• chr2-34017935-C-A
• rs10495803
• ENST00000366209.6:n.389+73382C>A

Variant summary

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

The ENST00000442026.1(LINC01320):​n.471-42815C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.343 in 151,856 control chromosomes in the GnomAD database, including 9,511 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 0.34 (9511 hom., cov: 31)
• Consequence: LINC01320 ENST00000442026.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.173
• Publications: 1 publications found

Genes affected

LINC01320 (HGNC:50526): (long intergenic non-protein coding RNA 1320)

LINC01317 (HGNC:50523): (long intergenic non-protein coding RNA 1317)

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 (SAS) allele frequency at 95% confidence interval = 0.451 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000442026.1. 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
	LINC01317	NR_126403.1		n.389+73382C>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01320	ENST00000366209.6	TSL:5	n.389+73382C>A		intron	N/A
	LINC01320	ENST00000442026.1	TSL:3	n.471-42815C>A		intron	N/A
	LINC01320	ENST00000771863.1		n.266-43084C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.343 AC: 52090 AN: 151736 Hom.: 9512 Cov.: 31

Gnomad AFR AF: 0.201

Gnomad AMI AF: 0.604

Gnomad AMR AF: 0.359

Gnomad ASJ AF: 0.400

Gnomad EAS AF: 0.367

Gnomad SAS AF: 0.466

Gnomad FIN AF: 0.438

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.393

Gnomad OTH AF: 0.378

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

GnomAD4 genome AF: 0.343 AC: 52083 AN: 151856 Hom.: 9511 Cov.: 31 AF XY: 0.349 AC XY: 25871 AN XY: 74196

African (AFR) AF: 0.200 AC: 8278 AN: 41376

American (AMR) AF: 0.358 AC: 5464 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.400 AC: 1386 AN: 3468

East Asian (EAS) AF: 0.368 AC: 1897 AN: 5156

South Asian (SAS) AF: 0.467 AC: 2251 AN: 4824

European-Finnish (FIN) AF: 0.438 AC: 4616 AN: 10528

Middle Eastern (MID) AF: 0.412 AC: 121 AN: 294

European-Non Finnish (NFE) AF: 0.393 AC: 26730 AN: 67946

Other (OTH) AF: 0.375 AC: 790 AN: 2106

Alfa AF: 0.355 Hom.: 1241

Bravo AF: 0.326

Asia WGS AF: 0.362 AC: 1260 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	2.0
DANN	Benign	0.65
PhyloP100		-0.17

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: rs10495803;

hg19: chr2-34243002;