rs2279839

Variant names:

• chr2-113977812-T-C
• rs2279839
• NR_034130.1:n.2173A>G

Variant summary

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

The NR_034130.1(LINC02992):​n.2173A>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 0.437 in 150,932 control chromosomes in the GnomAD database, including 17,686 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 0.44 (17686 hom., cov: 32)
• Consequence: LINC02992 NR_034130.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0190
• Publications: 4 publications found

Genes affected

LINC02992 (HGNC:49287): (long intergenic non-protein coding RNA 2992)

LINC01191 (HGNC:49595): (long intergenic non-protein coding RNA 1191)

ENSG00000307741 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.759 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02992	NR_034130.1	n.2173A>G		non_coding_transcript_exon_variant	Exon 1 of 1
LINC01191	NR_148507.1	n.407+7059T>C		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01191	ENST00000663402.1	n.35+7059T>C		intron_variant	Intron 1 of 2
LINC01191	ENST00000828061.1	n.133+7059T>C		intron_variant	Intron 1 of 1
ENSG00000307741	ENST00000828396.1	n.*214A>G		downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.436 AC: 65780 AN: 150812 Hom.: 17644 Cov.: 32

Gnomad AFR AF: 0.766

Gnomad AMI AF: 0.371

Gnomad AMR AF: 0.372

Gnomad ASJ AF: 0.284

Gnomad EAS AF: 0.0979

Gnomad SAS AF: 0.364

Gnomad FIN AF: 0.378

Gnomad MID AF: 0.261

Gnomad NFE AF: 0.299

Gnomad OTH AF: 0.393

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

GnomAD4 genome AF: 0.437 AC: 65889 AN: 150932 Hom.: 17686 Cov.: 32 AF XY: 0.434 AC XY: 32050 AN XY: 73766

African (AFR) AF: 0.766 AC: 31630 AN: 41294

American (AMR) AF: 0.372 AC: 5658 AN: 15194

Ashkenazi Jewish (ASJ) AF: 0.284 AC: 981 AN: 3450

East Asian (EAS) AF: 0.0975 AC: 490 AN: 5026

South Asian (SAS) AF: 0.365 AC: 1735 AN: 4752

European-Finnish (FIN) AF: 0.378 AC: 3978 AN: 10518

Middle Eastern (MID) AF: 0.266 AC: 77 AN: 290

European-Non Finnish (NFE) AF: 0.299 AC: 20179 AN: 67406

Other (OTH) AF: 0.394 AC: 826 AN: 2098

Alfa AF: 0.396 Hom.: 6181

Bravo AF: 0.454

Asia WGS AF: 0.274 AC: 953 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	5.5
DANN	Benign	0.58
PhyloP100		-0.019

Splicing

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

Other links and lift over

dbSNP: rs2279839; hg19: chr2-114735389; COSMIC: COSV69715752;