2-242106609-C-T

Variant names:

• chr2-242106609-C-T
• rs12478296
• ENST00000416103.2:n.135-8030C>T

Variant summary

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

The ENST00000614114.4(ENSG00000291147):​n.248-8030C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.208 in 151,932 control chromosomes in the GnomAD database, including 4,157 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 (4157 hom., cov: 32)
• Consequence: ENSG00000291147 ENST00000614114.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.289

Genes affected

LINC01881 (HGNC:52700): (long intergenic non-protein coding RNA 1881)

ENSG00000291147 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.405 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01881	NR_130699.1	n.311-8030C>T		intron_variant	Intron 2 of 7
LINC01881	NR_130700.1	n.310+11582C>T		intron_variant	Intron 2 of 5
LINC01881	NR_130701.1	n.311-8030C>T		intron_variant	Intron 2 of 7
LINC01881	NR_130702.1	n.311-8030C>T		intron_variant	Intron 2 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01881	ENST00000416103.2	n.135-8030C>T		intron_variant	Intron 1 of 4	6
ENSG00000291147	ENST00000431796.5	n.251-8030C>T		intron_variant	Intron 2 of 4	4
ENSG00000291147	ENST00000444990.7	n.306-8030C>T		intron_variant	Intron 2 of 3	3

Frequencies

GnomAD3 genomes AF: 0.207 AC: 31500 AN: 151814 Hom.: 4139 Cov.: 32

Gnomad AFR AF: 0.305

Gnomad AMI AF: 0.160

Gnomad AMR AF: 0.326

Gnomad ASJ AF: 0.144

Gnomad EAS AF: 0.420

Gnomad SAS AF: 0.316

Gnomad FIN AF: 0.172

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.107

Gnomad OTH AF: 0.196

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

GnomAD4 genome AF: 0.208 AC: 31549 AN: 151932 Hom.: 4157 Cov.: 32 AF XY: 0.216 AC XY: 16022 AN XY: 74274

Gnomad4 AFR AF: 0.305

Gnomad4 AMR AF: 0.328

Gnomad4 ASJ AF: 0.144

Gnomad4 EAS AF: 0.420

Gnomad4 SAS AF: 0.316

Gnomad4 FIN AF: 0.172

Gnomad4 NFE AF: 0.107

Gnomad4 OTH AF: 0.201

Alfa AF: 0.129 Hom.: 2292

Bravo AF: 0.222

Asia WGS AF: 0.379 AC: 1316 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	3.6
DANN	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12478296; hg19: chr2-243048760;