20-48366987-C-T

Variant names:

• chr20-48366987-C-T
• rs749044
• ENST00000416742.5:n.922C>T

Variant summary

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

The ENST00000416742.5(LINC00494):​n.922C>T 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 0.143 in 152,068 control chromosomes in the GnomAD database, including 2,396 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 0.14 (2396 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: LINC00494 ENST00000416742.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0920
• Publications: 7 publications found

Genes affected

LINC00494 (HGNC:27657): (long intergenic non-protein coding RNA 494)

ENSG00000286063 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.304 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00494	NR_026958.1	n.961C>T		non_coding_transcript_exon_variant	Exon 4 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00494	ENST00000416742.5	n.922C>T		non_coding_transcript_exon_variant	Exon 4 of 5	1
LINC00494	ENST00000433094.1	n.521+354C>T		intron_variant	Intron 2 of 2	1
LINC00494	ENST00000545181.5	n.721C>T		non_coding_transcript_exon_variant	Exon 3 of 4	5

Frequencies

GnomAD3 genomes AF: 0.143 AC: 21728 AN: 151950 Hom.: 2392 Cov.: 32

Gnomad AFR AF: 0.309

Gnomad AMI AF: 0.0735

Gnomad AMR AF: 0.0886

Gnomad ASJ AF: 0.117

Gnomad EAS AF: 0.143

Gnomad SAS AF: 0.0644

Gnomad FIN AF: 0.0621

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0757

Gnomad OTH AF: 0.121

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 2 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 2

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 2

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.143 AC: 21757 AN: 152068 Hom.: 2396 Cov.: 32 AF XY: 0.140 AC XY: 10418 AN XY: 74316

African (AFR) AF: 0.309 AC: 12801 AN: 41434

American (AMR) AF: 0.0885 AC: 1352 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.117 AC: 405 AN: 3470

East Asian (EAS) AF: 0.143 AC: 739 AN: 5168

South Asian (SAS) AF: 0.0636 AC: 307 AN: 4826

European-Finnish (FIN) AF: 0.0621 AC: 657 AN: 10580

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.0757 AC: 5148 AN: 67992

Other (OTH) AF: 0.120 AC: 254 AN: 2108

Alfa AF: 0.0872 Hom.: 506

Bravo AF: 0.155

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.4
DANN	Benign	0.59
PhyloP100		-0.092

Splicing

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

Other links and lift over

dbSNP: rs749044; hg19: chr20-46995730;