rs725600

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

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
LINC00540	ENST00000611481.1	n.165+63429A>G		intron_variant	Intron 1 of 1	4
LINC00540	ENST00000631321.1	n.411-103460A>G		intron_variant	Intron 1 of 1	2
LINC00540	ENST00000657205.1	n.414-12870A>G		intron_variant	Intron 1 of 3

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

Gnomad4 AFR AF: 0.712

Gnomad4 AMR AF: 0.689

Gnomad4 ASJ AF: 0.592

Gnomad4 EAS AF: 0.527

Gnomad4 SAS AF: 0.717

Gnomad4 FIN AF: 0.708

Gnomad4 NFE AF: 0.633

Gnomad4 OTH AF: 0.647

Alfa AF: 0.649 Hom.: 19261

Bravo AF: 0.664

Asia WGS AF: 0.635 AC: 2210 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	6.2
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs725600; hg19: chr13-22745202;