rs2074193

chr12-47377646-T-G

Variant summary

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

The ENST00000659658.1(LINC02156):n.9T>G 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 0.208 in 152,148 control chromosomes in the GnomAD database, including 3,505 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 0.21 (3505 hom., cov: 32)
• Consequence: LINC02156 ENST00000659658.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.295

Genes affected

LINC02156 (HGNC:53017): (long intergenic non-protein coding RNA 2156)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.242 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02156	ENST00000659658.1	n.9T>G		non_coding_transcript_exon_variant	1/3

Frequencies

GnomAD3 genomes AF: 0.208 AC: 31566 AN: 152032 Hom.: 3506 Cov.: 32

Gnomad AFR AF: 0.147

Gnomad AMI AF: 0.228

Gnomad AMR AF: 0.249

Gnomad ASJ AF: 0.222

Gnomad EAS AF: 0.0473

Gnomad SAS AF: 0.238

Gnomad FIN AF: 0.225

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.240

Gnomad OTH AF: 0.243

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

GnomAD4 genome AF: 0.208 AC: 31574 AN: 152148 Hom.: 3505 Cov.: 32 AF XY: 0.207 AC XY: 15432 AN XY: 74376

Gnomad4 AFR AF: 0.146

Gnomad4 AMR AF: 0.248

Gnomad4 ASJ AF: 0.222

Gnomad4 EAS AF: 0.0474

Gnomad4 SAS AF: 0.239

Gnomad4 FIN AF: 0.225

Gnomad4 NFE AF: 0.240

Gnomad4 OTH AF: 0.244

Alfa AF: 0.240 Hom.: 4383

Bravo AF: 0.207

Asia WGS AF: 0.172 AC: 599 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
Cadd	Benign	4.0
Dann	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2074193; hg19: chr12-47771429;