rs9552612

Variant names:

• chr13-22180439-C-A
• rs9552612
• ENST00000611481.1:n.165+72805C>A

Variant summary

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

The ENST00000611481.1(LINC00540):​n.165+72805C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.362 in 151,846 control chromosomes in the GnomAD database, including 10,154 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 0.36 (10154 hom., cov: 33)
• Consequence: LINC00540 ENST00000611481.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.551
• Publications: 2 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=-1.05).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.372 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+72805C>A		intron_variant	Intron 1 of 1	4
LINC00540	ENST00000631321.1	n.411-94084C>A		intron_variant	Intron 1 of 1	2
LINC00540	ENST00000657205.1	n.414-3494C>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.362 AC: 54969 AN: 151728 Hom.: 10150 Cov.: 33

Gnomad AFR AF: 0.375

Gnomad AMI AF: 0.454

Gnomad AMR AF: 0.372

Gnomad ASJ AF: 0.359

Gnomad EAS AF: 0.127

Gnomad SAS AF: 0.376

Gnomad FIN AF: 0.307

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.376

Gnomad OTH AF: 0.383

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

GnomAD4 genome AF: 0.362 AC: 55014 AN: 151846 Hom.: 10154 Cov.: 33 AF XY: 0.358 AC XY: 26588 AN XY: 74190

African (AFR) AF: 0.375 AC: 15543 AN: 41420

American (AMR) AF: 0.372 AC: 5680 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.359 AC: 1245 AN: 3466

East Asian (EAS) AF: 0.127 AC: 657 AN: 5168

South Asian (SAS) AF: 0.377 AC: 1814 AN: 4816

European-Finnish (FIN) AF: 0.307 AC: 3235 AN: 10524

Middle Eastern (MID) AF: 0.401 AC: 118 AN: 294

European-Non Finnish (NFE) AF: 0.376 AC: 25507 AN: 67886

Other (OTH) AF: 0.380 AC: 801 AN: 2110

Alfa AF: 0.378 Hom.: 6097

Bravo AF: 0.368

Asia WGS AF: 0.287 AC: 997 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.11
DANN	Benign	0.18
PhyloP100		-0.55

Splicing

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

Other links and lift over

dbSNP: rs9552612; hg19: chr13-22754578;