2-156180497-T-C

Variant names:

• chr2-156180497-T-C
• rs4637055
• ENST00000428651.2:n.159+74281A>G

Variant summary

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

The ENST00000637665.1(LINC01876):​n.138+74281A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.222 in 152,026 control chromosomes in the GnomAD database, including 4,081 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 0.22 (4081 hom., cov: 32)
• Consequence: LINC01876 ENST00000637665.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.527
• Publications: 3 publications found

Genes affected

LINC01876 (HGNC:52695): (long intergenic non-protein coding RNA 1876)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.351 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000637665.1. 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
	LINC01876	NR_110249.2		n.154+74281A>G		intron	N/A
	LINC01876	NR_110250.2		n.154+74281A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01876	ENST00000428651.2	TSL:5	n.159+74281A>G		intron	N/A
	LINC01876	ENST00000635799.1	TSL:5	n.152+74281A>G		intron	N/A
	LINC01876	ENST00000636956.1	TSL:5	n.268+24885A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.222 AC: 33724 AN: 151908 Hom.: 4060 Cov.: 32

Gnomad AFR AF: 0.146

Gnomad AMI AF: 0.213

Gnomad AMR AF: 0.209

Gnomad ASJ AF: 0.347

Gnomad EAS AF: 0.334

Gnomad SAS AF: 0.363

Gnomad FIN AF: 0.246

Gnomad MID AF: 0.210

Gnomad NFE AF: 0.243

Gnomad OTH AF: 0.226

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

GnomAD4 genome AF: 0.222 AC: 33786 AN: 152026 Hom.: 4081 Cov.: 32 AF XY: 0.225 AC XY: 16690 AN XY: 74306

African (AFR) AF: 0.146 AC: 6073 AN: 41486

American (AMR) AF: 0.209 AC: 3192 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.347 AC: 1205 AN: 3470

East Asian (EAS) AF: 0.334 AC: 1723 AN: 5154

South Asian (SAS) AF: 0.366 AC: 1759 AN: 4812

European-Finnish (FIN) AF: 0.246 AC: 2599 AN: 10562

Middle Eastern (MID) AF: 0.202 AC: 59 AN: 292

European-Non Finnish (NFE) AF: 0.243 AC: 16501 AN: 67964

Other (OTH) AF: 0.228 AC: 481 AN: 2110

Alfa AF: 0.129 Hom.: 241

Bravo AF: 0.215

Asia WGS AF: 0.338 AC: 1175 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	7.1
DANN	Benign	0.84
PhyloP100		0.53

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: rs4637055;

hg19: chr2-157037009;