13-22214725-C-T

Variant names:

• chr13-22214725-C-T
• rs7317667
• ENST00000616974.1:n.144+4297C>T

Variant summary

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

The ENST00000616974.1(LINC00540):​n.144+4297C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0686 in 152,018 control chromosomes in the GnomAD database, including 1,144 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 0.069 (1144 hom., cov: 32)
• Consequence: LINC00540 ENST00000616974.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.14
• Publications: 0 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=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.222 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00540	NR_103810.1	n.144+4297C>T		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00540	ENST00000616974.1	n.144+4297C>T		intron_variant	Intron 1 of 1	1
LINC00540	ENST00000611481.1	n.166-59798C>T		intron_variant	Intron 1 of 1	4
LINC00540	ENST00000631321.1	n.411-59798C>T		intron_variant	Intron 1 of 1	2

Frequencies

GnomAD3 genomes AF: 0.0685 AC: 10408 AN: 151900 Hom.: 1142 Cov.: 32

Gnomad AFR AF: 0.226

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0294

Gnomad ASJ AF: 0.00404

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0106

Gnomad FIN AF: 0.0107

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.00469

Gnomad OTH AF: 0.0551

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

GnomAD4 genome AF: 0.0686 AC: 10428 AN: 152018 Hom.: 1144 Cov.: 32 AF XY: 0.0654 AC XY: 4863 AN XY: 74316

African (AFR) AF: 0.226 AC: 9358 AN: 41406

American (AMR) AF: 0.0294 AC: 449 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.00404 AC: 14 AN: 3464

East Asian (EAS) AF: 0.000386 AC: 2 AN: 5180

South Asian (SAS) AF: 0.0108 AC: 52 AN: 4812

European-Finnish (FIN) AF: 0.0107 AC: 113 AN: 10584

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.00468 AC: 318 AN: 67988

Other (OTH) AF: 0.0546 AC: 115 AN: 2108

Alfa AF: 0.0718 Hom.: 607

Bravo AF: 0.0783

Asia WGS AF: 0.0160 AC: 54 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	6.5
DANN	Benign	0.68
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs7317667; hg19: chr13-22788864;