ENST00000652995.1:n.399-21096G>A

Variant names:

• chr2-176618395-G-A
• rs2969363
• ENST00000652995.1:n.399-21096G>A

Variant summary

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

The ENST00000652995.1(LINC01117):​n.399-21096G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.552 in 152,036 control chromosomes in the GnomAD database, including 24,894 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 0.55 (24894 hom., cov: 32)
• Consequence: LINC01117 ENST00000652995.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.215
• Publications: 5 publications found

Genes affected

LINC01117 (HGNC:49260): (long intergenic non-protein coding RNA 1117)

LINC01116 (HGNC:49259): (long intergenic non-protein coding RNA 1116)

ENSG00000306034 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.798 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01116	NR_188021.1	n.363-4615C>T		intron_variant	Intron 3 of 3
LINC01116	NR_188022.1	n.363-1770C>T		intron_variant	Intron 3 of 4
LINC01116	NR_188023.1	n.482+4222C>T		intron_variant	Intron 4 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01117	ENST00000652995.1	n.399-21096G>A		intron_variant	Intron 2 of 3
LINC01116	ENST00000695928.2	n.529-1770C>T		intron_variant	Intron 3 of 4
LINC01117	ENST00000814385.1	n.186-21096G>A		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.552 AC: 83853 AN: 151918 Hom.: 24889 Cov.: 32

Gnomad AFR AF: 0.324

Gnomad AMI AF: 0.754

Gnomad AMR AF: 0.698

Gnomad ASJ AF: 0.647

Gnomad EAS AF: 0.818

Gnomad SAS AF: 0.475

Gnomad FIN AF: 0.615

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.625

Gnomad OTH AF: 0.568

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

GnomAD4 genome AF: 0.552 AC: 83873 AN: 152036 Hom.: 24894 Cov.: 32 AF XY: 0.554 AC XY: 41180 AN XY: 74306

African (AFR) AF: 0.323 AC: 13409 AN: 41472

American (AMR) AF: 0.699 AC: 10670 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.647 AC: 2247 AN: 3472

East Asian (EAS) AF: 0.818 AC: 4228 AN: 5168

South Asian (SAS) AF: 0.476 AC: 2289 AN: 4812

European-Finnish (FIN) AF: 0.615 AC: 6487 AN: 10544

Middle Eastern (MID) AF: 0.514 AC: 151 AN: 294

European-Non Finnish (NFE) AF: 0.625 AC: 42519 AN: 67988

Other (OTH) AF: 0.564 AC: 1187 AN: 2106

Alfa AF: 0.606 Hom.: 91733

Bravo AF: 0.555

Asia WGS AF: 0.648 AC: 2252 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.5
DANN	Benign	0.64
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs2969363; hg19: chr2-177483123;