2-242106609-C-T

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 11 publications found

Genes affected

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

ENSG00000291147 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000614114.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01881	NR_130699.1		n.311-8030C>T		intron	N/A
	LINC01881	NR_130700.1		n.310+11582C>T		intron	N/A
	LINC01881	NR_130701.1		n.311-8030C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01881	ENST00000416103.2	TSL:6	n.135-8030C>T		intron	N/A
	ENSG00000291147	ENST00000431796.6	TSL:4	n.260-8030C>T		intron	N/A
	ENSG00000291147	ENST00000433444.2	TSL:3	n.285-8030C>T		intron	N/A

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

African (AFR) AF: 0.305 AC: 12626 AN: 41396

American (AMR) AF: 0.328 AC: 4994 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.144 AC: 499 AN: 3472

East Asian (EAS) AF: 0.420 AC: 2170 AN: 5168

South Asian (SAS) AF: 0.316 AC: 1517 AN: 4806

European-Finnish (FIN) AF: 0.172 AC: 1824 AN: 10576

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.107 AC: 7300 AN: 67964

Other (OTH) AF: 0.201 AC: 422 AN: 2100

Alfa AF: 0.135 Hom.: 3344

Bravo AF: 0.222

Asia WGS AF: 0.379 AC: 1316 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	3.6
DANN	Benign	0.84
PhyloP100		0.29

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs12478296;

hg19: chr2-243048760;