rs17326684

Variant names:

• chr13-22195400-G-A
• rs17326684
• ENST00000611481.1:n.166-79123G>A

Variant summary

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

The ENST00000611481.1(LINC00540):​n.166-79123G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.232 in 151,924 control chromosomes in the GnomAD database, including 4,607 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 0.23 (4607 hom., cov: 33)
• Consequence: LINC00540 ENST00000611481.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.378
• Publications: 1 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=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.326 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.166-79123G>A		intron_variant	Intron 1 of 1	4
LINC00540	ENST00000631321.1	n.411-79123G>A		intron_variant	Intron 1 of 1	2
LINC00540	ENST00000657205.1	n.481+11400G>A		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.232 AC: 35266 AN: 151806 Hom.: 4610 Cov.: 33

Gnomad AFR AF: 0.127

Gnomad AMI AF: 0.284

Gnomad AMR AF: 0.272

Gnomad ASJ AF: 0.308

Gnomad EAS AF: 0.133

Gnomad SAS AF: 0.340

Gnomad FIN AF: 0.249

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.279

Gnomad OTH AF: 0.245

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

GnomAD4 genome AF: 0.232 AC: 35280 AN: 151924 Hom.: 4607 Cov.: 33 AF XY: 0.234 AC XY: 17333 AN XY: 74226

African (AFR) AF: 0.127 AC: 5267 AN: 41428

American (AMR) AF: 0.272 AC: 4158 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.308 AC: 1069 AN: 3472

East Asian (EAS) AF: 0.133 AC: 687 AN: 5156

South Asian (SAS) AF: 0.340 AC: 1634 AN: 4808

European-Finnish (FIN) AF: 0.249 AC: 2611 AN: 10492

Middle Eastern (MID) AF: 0.293 AC: 86 AN: 294

European-Non Finnish (NFE) AF: 0.279 AC: 18996 AN: 67968

Other (OTH) AF: 0.243 AC: 513 AN: 2110

Alfa AF: 0.274 Hom.: 8278

Bravo AF: 0.228

Asia WGS AF: 0.260 AC: 907 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.4
DANN	Benign	0.64
PhyloP100		-0.38

Splicing

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

Other links and lift over

dbSNP: rs17326684; hg19: chr13-22769539;