rs934956

chr2-104480671-G-Achr2-104480671-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_015399.1(LINC01102):n.178-25195G>A variant causes a intron, non coding transcript 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 NR_015399.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.91

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LINC01102	NR_015399.1	n.178-25195G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01102	ENST00000690368.1	n.184-25195G>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.415

Gnomad4 AMR AF: 0.226

Gnomad4 ASJ AF: 0.251

Gnomad4 EAS AF: 0.182

Gnomad4 SAS AF: 0.246

Gnomad4 FIN AF: 0.204

Gnomad4 NFE AF: 0.290

Gnomad4 OTH AF: 0.283

Alfa AF: 0.277 Hom.: 11855

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs934956; hg19: chr2-105097129;