ENST00000447380.2:n.147-25195G>A

Variant names:

• chr2-104480671-G-A
• rs934956
• ENST00000447380.2:n.147-25195G>A

Variant summary

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

The ENST00000447380.2(LINC01102):​n.147-25195G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.306 in 152,010 control chromosomes in the GnomAD database, including 7,634 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 0.31 (7634 hom., cov: 32)
• Consequence: LINC01102 ENST00000447380.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.91
• Publications: 2 publications found

Genes affected

LINC01102 (HGNC:27165): (long intergenic non-protein coding RNA 1102)

ENSG00000293648 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.41 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01102	NR_015399.1	n.178-25195G>A		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01102	ENST00000447380.2	n.147-25195G>A		intron_variant	Intron 1 of 4	1
LINC01102	ENST00000414442.2	n.217-25195G>A		intron_variant	Intron 1 of 1	3
LINC01102	ENST00000429464.1	n.163-25195G>A		intron_variant	Intron 1 of 1	2

Frequencies

GnomAD3 genomes AF: 0.306 AC: 46474 AN: 151892 Hom.: 7631 Cov.: 32

Gnomad AFR AF: 0.415

Gnomad AMI AF: 0.402

Gnomad AMR AF: 0.226

Gnomad ASJ AF: 0.251

Gnomad EAS AF: 0.181

Gnomad SAS AF: 0.247

Gnomad FIN AF: 0.204

Gnomad MID AF: 0.242

Gnomad NFE AF: 0.290

Gnomad OTH AF: 0.284

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

GnomAD4 genome AF: 0.306 AC: 46503 AN: 152010 Hom.: 7634 Cov.: 32 AF XY: 0.301 AC XY: 22329 AN XY: 74282

African (AFR) AF: 0.415 AC: 17181 AN: 41428

American (AMR) AF: 0.226 AC: 3449 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.251 AC: 871 AN: 3470

East Asian (EAS) AF: 0.182 AC: 939 AN: 5158

South Asian (SAS) AF: 0.246 AC: 1186 AN: 4818

European-Finnish (FIN) AF: 0.204 AC: 2162 AN: 10574

Middle Eastern (MID) AF: 0.240 AC: 70 AN: 292

European-Non Finnish (NFE) AF: 0.290 AC: 19682 AN: 67954

Other (OTH) AF: 0.283 AC: 597 AN: 2112

Alfa AF: 0.286 Hom.: 20194

Bravo AF: 0.310

Asia WGS AF: 0.202 AC: 705 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.012
DANN	Benign	0.39
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs934956; hg19: chr2-105097129;