13-22253613-C-T

Variant names:

• chr13-22253613-C-T
• rs1408051
• ENST00000616974.1:n.145-20910C>T

Variant summary

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

The ENST00000616974.1(LINC00540):​n.145-20910C>T 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 152,072 control chromosomes in the GnomAD database, including 33,919 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 (33919 hom., cov: 32)
• Consequence: LINC00540 ENST00000616974.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0170
• Publications: 8 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=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.735 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00540	NR_103810.1	n.145-20910C>T		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00540	ENST00000616974.1	n.145-20910C>T		intron_variant	Intron 1 of 1	1
LINC00540	ENST00000611481.1	n.166-20910C>T		intron_variant	Intron 1 of 1	4
LINC00540	ENST00000631321.1	n.411-20910C>T		intron_variant	Intron 1 of 1	2

Frequencies

GnomAD3 genomes AF: 0.663 AC: 100809 AN: 151952 Hom.: 33863 Cov.: 32

Gnomad AFR AF: 0.742

Gnomad AMI AF: 0.601

Gnomad AMR AF: 0.659

Gnomad ASJ AF: 0.502

Gnomad EAS AF: 0.752

Gnomad SAS AF: 0.663

Gnomad FIN AF: 0.703

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.614

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: 100925 AN: 152072 Hom.: 33919 Cov.: 32 AF XY: 0.668 AC XY: 49656 AN XY: 74322

African (AFR) AF: 0.742 AC: 30792 AN: 41490

American (AMR) AF: 0.660 AC: 10086 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.502 AC: 1742 AN: 3468

East Asian (EAS) AF: 0.752 AC: 3885 AN: 5168

South Asian (SAS) AF: 0.662 AC: 3197 AN: 4826

European-Finnish (FIN) AF: 0.703 AC: 7437 AN: 10574

Middle Eastern (MID) AF: 0.493 AC: 145 AN: 294

European-Non Finnish (NFE) AF: 0.614 AC: 41723 AN: 67958

Other (OTH) AF: 0.651 AC: 1372 AN: 2108

Alfa AF: 0.625 Hom.: 59338

Bravo AF: 0.663

Asia WGS AF: 0.750 AC: 2608 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.6
DANN	Benign	0.49
PhyloP100		0.017

Splicing

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

Other links and lift over

dbSNP: rs1408051; hg19: chr13-22827752;