ENST00000652227.1:n.494+38660A>T

Variant names:

• chr2-176694438-A-T
• rs16864244
• ENST00000652227.1:n.494+38660A>T

Variant summary

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

The ENST00000652227.1(LINC01117):​n.494+38660A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.126 in 151,872 control chromosomes in the GnomAD database, including 1,330 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 0.13 (1330 hom., cov: 32)
• Consequence: LINC01117 ENST00000652227.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.432
• Publications: 1 publications found

Genes affected

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

ENSG00000230552 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.54).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.183 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01117	ENST00000652227.1	n.494+38660A>T		intron_variant	Intron 4 of 5
LINC01117	ENST00000702503.1	n.370-53188A>T		intron_variant	Intron 2 of 4
LINC01117	ENST00000702732.2	n.385+54865A>T		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.126 AC: 19109 AN: 151754 Hom.: 1330 Cov.: 32

Gnomad AFR AF: 0.186

Gnomad AMI AF: 0.0912

Gnomad AMR AF: 0.0997

Gnomad ASJ AF: 0.209

Gnomad EAS AF: 0.00174

Gnomad SAS AF: 0.133

Gnomad FIN AF: 0.0920

Gnomad MID AF: 0.172

Gnomad NFE AF: 0.105

Gnomad OTH AF: 0.145

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

GnomAD4 genome AF: 0.126 AC: 19119 AN: 151872 Hom.: 1330 Cov.: 32 AF XY: 0.124 AC XY: 9177 AN XY: 74246

African (AFR) AF: 0.186 AC: 7720 AN: 41442

American (AMR) AF: 0.0997 AC: 1520 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.209 AC: 723 AN: 3464

East Asian (EAS) AF: 0.00174 AC: 9 AN: 5168

South Asian (SAS) AF: 0.133 AC: 637 AN: 4806

European-Finnish (FIN) AF: 0.0920 AC: 972 AN: 10560

Middle Eastern (MID) AF: 0.161 AC: 47 AN: 292

European-Non Finnish (NFE) AF: 0.105 AC: 7104 AN: 67866

Other (OTH) AF: 0.144 AC: 304 AN: 2112

Alfa AF: 0.122 Hom.: 150

Bravo AF: 0.127

Asia WGS AF: 0.0640 AC: 222 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.54
CADD	Benign	16
DANN	Benign	0.90
PhyloP100		0.43

Splicing

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

Other links and lift over

dbSNP: rs16864244; hg19: chr2-177559166;