rs2279839

chr2-113977812-T-C

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

LINC02992 (HGNC:):

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LINC02992	NR_034130.1	n.2173A>G		non_coding_transcript_exon_variant	1/1
LINC01191	NR_148507.1	n.407+7059T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01191	ENST00000663402.1	n.35+7059T>C		intron_variant, non_coding_transcript_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

Gnomad4 AFR AF: 0.766

Gnomad4 AMR AF: 0.372

Gnomad4 ASJ AF: 0.284

Gnomad4 EAS AF: 0.0975

Gnomad4 SAS AF: 0.365

Gnomad4 FIN AF: 0.378

Gnomad4 NFE AF: 0.299

Gnomad4 OTH AF: 0.394

Alfa AF: 0.393 Hom.: 5035

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

Splicing

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

Publications

LitVar

Other links and lift over

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