rs725600

Variant names:

• chr13-22171063-A-G
• rs725600
• ENST00000611481.1:n.165+63429A>G

Variant summary

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

The ENST00000631321.1(LINC00540):​n.411-103460A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.664 in 152,132 control chromosomes in the GnomAD database, including 33,642 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 0.66 (33642 hom., cov: 32)
• Consequence: LINC00540 ENST00000631321.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.598
• Publications: 4 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=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.705 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000631321.1. 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
	LINC00540	ENST00000611481.1	TSL:4	n.165+63429A>G		intron	N/A
	LINC00540	ENST00000631321.1	TSL:2	n.411-103460A>G		intron	N/A
	LINC00540	ENST00000657205.1		n.414-12870A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.664 AC: 100888 AN: 152014 Hom.: 33593 Cov.: 32

Gnomad AFR AF: 0.711

Gnomad AMI AF: 0.649

Gnomad AMR AF: 0.688

Gnomad ASJ AF: 0.592

Gnomad EAS AF: 0.529

Gnomad SAS AF: 0.718

Gnomad FIN AF: 0.708

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.633

Gnomad OTH AF: 0.647

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

GnomAD4 genome AF: 0.664 AC: 100998 AN: 152132 Hom.: 33642 Cov.: 32 AF XY: 0.670 AC XY: 49825 AN XY: 74362

African (AFR) AF: 0.712 AC: 29525 AN: 41482

American (AMR) AF: 0.689 AC: 10529 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.592 AC: 2052 AN: 3466

East Asian (EAS) AF: 0.527 AC: 2728 AN: 5172

South Asian (SAS) AF: 0.717 AC: 3453 AN: 4818

European-Finnish (FIN) AF: 0.708 AC: 7497 AN: 10584

Middle Eastern (MID) AF: 0.609 AC: 179 AN: 294

European-Non Finnish (NFE) AF: 0.633 AC: 43080 AN: 68006

Other (OTH) AF: 0.647 AC: 1366 AN: 2110

Alfa AF: 0.647 Hom.: 26146

Bravo AF: 0.664

Asia WGS AF: 0.635 AC: 2210 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	6.2
DANN	Benign	0.63
PhyloP100		0.60

Splicing

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

Other links and lift over

dbSNP: rs725600; hg19: chr13-22745202;