rs2074193

Variant names:

• chr12-47377646-T-G
• rs2074193
• ENST00000659658.1:n.9T>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 13 publications found

Genes affected

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

LINC02416 (HGNC:53345): (long intergenic non-protein coding RNA 2416)

ENSG00000310242 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02156	ENST00000659658.1	n.9T>G		non_coding_transcript_exon_variant	Exon 1 of 3
LINC02416	ENST00000718403.1	n.308+10222T>G		intron_variant	Intron 2 of 2
LINC02416	ENST00000718404.1	n.94-10538T>G		intron_variant	Intron 1 of 1

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

African (AFR) AF: 0.146 AC: 6081 AN: 41526

American (AMR) AF: 0.248 AC: 3792 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.222 AC: 771 AN: 3468

East Asian (EAS) AF: 0.0474 AC: 245 AN: 5170

South Asian (SAS) AF: 0.239 AC: 1154 AN: 4828

European-Finnish (FIN) AF: 0.225 AC: 2375 AN: 10568

Middle Eastern (MID) AF: 0.293 AC: 86 AN: 294

European-Non Finnish (NFE) AF: 0.240 AC: 16346 AN: 68000

Other (OTH) AF: 0.244 AC: 516 AN: 2114

Alfa AF: 0.236 Hom.: 5618

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
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs2074193; hg19: chr12-47771429;