13-75932669-T-G

Position:

• chr13-75932669-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_047491.1(LINC00561):​n.2464A>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.15 in 152,108 control chromosomes in the GnomAD database, including 1,818 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 0.15 (1818 hom., cov: 32)
  • Exomes 𝑓: 0.063 (0 hom.)
• Consequence: LINC00561 NR_047491.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.294

Genes affected

LINC00561 (HGNC:43705): (long intergenic non-protein coding RNA 561)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.203 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC00561	NR_047491.1	n.2464A>C		non_coding_transcript_exon_variant	1/1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00561	ENST00000565815.1	n.2464A>C		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.150 AC: 22845 AN: 151974 Hom.: 1818 Cov.: 32

Gnomad AFR AF: 0.159

Gnomad AMI AF: 0.157

Gnomad AMR AF: 0.209

Gnomad ASJ AF: 0.0600

Gnomad EAS AF: 0.138

Gnomad SAS AF: 0.0728

Gnomad FIN AF: 0.151

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.143

Gnomad OTH AF: 0.143

GnomAD4 exome AF: 0.0625 AC: 1 AN: 16 Hom.: 0 Cov.: 0 AF XY: 0.100 AC XY: 1 AN XY: 10

Gnomad4 NFE exome AF: 0.0625

GnomAD4 genome AF: 0.150 AC: 22862 AN: 152092 Hom.: 1818 Cov.: 32 AF XY: 0.149 AC XY: 11111 AN XY: 74346

Gnomad4 AFR AF: 0.159

Gnomad4 AMR AF: 0.210

Gnomad4 ASJ AF: 0.0600

Gnomad4 EAS AF: 0.138

Gnomad4 SAS AF: 0.0720

Gnomad4 FIN AF: 0.151

Gnomad4 NFE AF: 0.143

Gnomad4 OTH AF: 0.141

Alfa AF: 0.142 Hom.: 2236

Bravo AF: 0.157

Asia WGS AF: 0.122 AC: 424 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	3.3
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7317138; hg19: chr13-76506805;