rs2503340

Variant names:

• chr13-22236825-C-A
• rs2503340
• ENST00000616974.1:n.144+26397C>A

Variant summary

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

The ENST00000616974.1(LINC00540):​n.144+26397C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.771 in 152,130 control chromosomes in the GnomAD database, including 45,649 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 0.77 (45649 hom., cov: 32)
• Consequence: LINC00540 ENST00000616974.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.107
• Publications: 5 publications found

Genes affected

LINC00540 (HGNC:43673): (long intergenic non-protein coding RNA 540)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.824 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000616974.1. 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
	LINC00540	NR_103810.1		n.144+26397C>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00540	ENST00000616974.1	TSL:1	n.144+26397C>A		intron	N/A
	LINC00540	ENST00000611481.1	TSL:4	n.166-37698C>A		intron	N/A
	LINC00540	ENST00000631321.1	TSL:2	n.411-37698C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.771 AC: 117199 AN: 152012 Hom.: 45630 Cov.: 32

Gnomad AFR AF: 0.655

Gnomad AMI AF: 0.801

Gnomad AMR AF: 0.772

Gnomad ASJ AF: 0.770

Gnomad EAS AF: 0.780

Gnomad SAS AF: 0.775

Gnomad FIN AF: 0.836

Gnomad MID AF: 0.766

Gnomad NFE AF: 0.830

Gnomad OTH AF: 0.766

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

GnomAD4 genome AF: 0.771 AC: 117268 AN: 152130 Hom.: 45649 Cov.: 32 AF XY: 0.771 AC XY: 57355 AN XY: 74368

African (AFR) AF: 0.655 AC: 27167 AN: 41474

American (AMR) AF: 0.771 AC: 11798 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.770 AC: 2672 AN: 3472

East Asian (EAS) AF: 0.781 AC: 4026 AN: 5156

South Asian (SAS) AF: 0.775 AC: 3735 AN: 4822

European-Finnish (FIN) AF: 0.836 AC: 8849 AN: 10580

Middle Eastern (MID) AF: 0.759 AC: 223 AN: 294

European-Non Finnish (NFE) AF: 0.830 AC: 56451 AN: 68016

Other (OTH) AF: 0.766 AC: 1618 AN: 2112

Alfa AF: 0.807 Hom.: 205587

Bravo AF: 0.759

Asia WGS AF: 0.784 AC: 2729 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.3
DANN	Benign	0.49
PhyloP100		-0.11

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: rs2503340;

hg19: chr13-22810964;