ENST00000561513.6:n.1689T>C

Variant names:

• chr16-52083097-A-G
• rs2278016
• ENST00000561513.6:n.1689T>C

Variant summary

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

The ENST00000561513.6(LINC00919):​n.1689T>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 0.152 in 152,200 control chromosomes in the GnomAD database, including 1,974 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 (1974 hom., cov: 33)
  • Failed GnomAD Quality Control
• Consequence: LINC00919 ENST00000561513.6 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.381
• Publications: 3 publications found

Genes affected

LINC00919 (HGNC:48610): (long intergenic non-protein coding RNA 919)

LINC02180 (HGNC:53042): (long intergenic non-protein coding RNA 2180)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.204 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00919	NR_038233.1	n.1626T>C		non_coding_transcript_exon_variant	Exon 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00919	ENST00000561513.6	n.1689T>C		non_coding_transcript_exon_variant	Exon 3 of 3	2
LINC00919	ENST00000565742.1	n.1514T>C		non_coding_transcript_exon_variant	Exon 2 of 2	2
LINC00919	ENST00000655537.2	n.1581T>C		non_coding_transcript_exon_variant	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.153 AC: 23202 AN: 152082 Hom.: 1976 Cov.: 33

Gnomad AFR AF: 0.0825

Gnomad AMI AF: 0.118

Gnomad AMR AF: 0.210

Gnomad ASJ AF: 0.186

Gnomad EAS AF: 0.126

Gnomad SAS AF: 0.129

Gnomad FIN AF: 0.156

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.184

Gnomad OTH AF: 0.165

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

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) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.152 AC: 23206 AN: 152200 Hom.: 1974 Cov.: 33 AF XY: 0.150 AC XY: 11132 AN XY: 74390

African (AFR) AF: 0.0823 AC: 3421 AN: 41560

American (AMR) AF: 0.210 AC: 3199 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.186 AC: 643 AN: 3466

East Asian (EAS) AF: 0.127 AC: 654 AN: 5162

South Asian (SAS) AF: 0.130 AC: 625 AN: 4824

European-Finnish (FIN) AF: 0.156 AC: 1655 AN: 10616

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.184 AC: 12536 AN: 67994

Other (OTH) AF: 0.161 AC: 340 AN: 2112

Alfa AF: 0.169 Hom.: 487

Bravo AF: 0.157

Asia WGS AF: 0.129 AC: 448 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	8.7
DANN	Benign	0.89
PhyloP100		0.38
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs2278016; hg19: chr16-52117009;