13-22248588-T-C

Variant names:

• chr13-22248588-T-C
• rs7328193
• ENST00000616974.1:n.145-25935T>C

Variant summary

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

The ENST00000616974.1(LINC00540):​n.145-25935T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.808 in 152,224 control chromosomes in the GnomAD database, including 49,864 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 0.81 (49864 hom., cov: 34)
• Consequence: LINC00540 ENST00000616974.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.524
• Publications: 6 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=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.841 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00540	NR_103810.1	n.145-25935T>C		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00540	ENST00000616974.1	n.145-25935T>C		intron_variant	Intron 1 of 1	1
LINC00540	ENST00000611481.1	n.166-25935T>C		intron_variant	Intron 1 of 1	4
LINC00540	ENST00000631321.1	n.411-25935T>C		intron_variant	Intron 1 of 1	2

Frequencies

GnomAD3 genomes AF: 0.808 AC: 122905 AN: 152106 Hom.: 49829 Cov.: 34

Gnomad AFR AF: 0.785

Gnomad AMI AF: 0.630

Gnomad AMR AF: 0.758

Gnomad ASJ AF: 0.806

Gnomad EAS AF: 0.633

Gnomad SAS AF: 0.795

Gnomad FIN AF: 0.829

Gnomad MID AF: 0.785

Gnomad NFE AF: 0.847

Gnomad OTH AF: 0.810

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

GnomAD4 genome AF: 0.808 AC: 122988 AN: 152224 Hom.: 49864 Cov.: 34 AF XY: 0.803 AC XY: 59781 AN XY: 74410

African (AFR) AF: 0.786 AC: 32629 AN: 41538

American (AMR) AF: 0.756 AC: 11562 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.806 AC: 2793 AN: 3466

East Asian (EAS) AF: 0.634 AC: 3280 AN: 5176

South Asian (SAS) AF: 0.794 AC: 3832 AN: 4826

European-Finnish (FIN) AF: 0.829 AC: 8773 AN: 10580

Middle Eastern (MID) AF: 0.776 AC: 228 AN: 294

European-Non Finnish (NFE) AF: 0.847 AC: 57606 AN: 68034

Other (OTH) AF: 0.811 AC: 1712 AN: 2112

Alfa AF: 0.828 Hom.: 140365

Bravo AF: 0.800

Asia WGS AF: 0.709 AC: 2467 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	6.5
DANN	Benign	0.38
PhyloP100		0.52

Splicing

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

Other links and lift over

dbSNP: rs7328193; hg19: chr13-22822727;