2-156068774-A-T

Variant names:

• chr2-156068774-A-T
• rs16839962
• ENST00000428651.2:n.160-44198T>A

Variant summary

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

The ENST00000428651.2(LINC01876):​n.160-44198T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.147 in 152,006 control chromosomes in the GnomAD database, including 2,136 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 0.15 (2136 hom., cov: 32)
• Consequence: LINC01876 ENST00000428651.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.167
• Publications: 10 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=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.499 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01876	NR_110249.2	n.155-44198T>A		intron_variant	Intron 1 of 3
LINC01876	NR_110250.2	n.155-44167T>A		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01876	ENST00000428651.2	n.160-44198T>A		intron_variant	Intron 1 of 3	5
LINC01876	ENST00000635799.1	n.153-44198T>A		intron_variant	Intron 1 of 4	5
LINC01876	ENST00000636956.1	n.269-44167T>A		intron_variant	Intron 3 of 5	5

Frequencies

GnomAD3 genomes AF: 0.147 AC: 22306 AN: 151888 Hom.: 2128 Cov.: 32

Gnomad AFR AF: 0.121

Gnomad AMI AF: 0.0899

Gnomad AMR AF: 0.163

Gnomad ASJ AF: 0.236

Gnomad EAS AF: 0.516

Gnomad SAS AF: 0.202

Gnomad FIN AF: 0.122

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.127

Gnomad OTH AF: 0.162

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

GnomAD4 genome AF: 0.147 AC: 22340 AN: 152006 Hom.: 2136 Cov.: 32 AF XY: 0.149 AC XY: 11110 AN XY: 74326

African (AFR) AF: 0.121 AC: 5040 AN: 41526

American (AMR) AF: 0.163 AC: 2477 AN: 15216

Ashkenazi Jewish (ASJ) AF: 0.236 AC: 818 AN: 3466

East Asian (EAS) AF: 0.516 AC: 2655 AN: 5150

South Asian (SAS) AF: 0.201 AC: 970 AN: 4820

European-Finnish (FIN) AF: 0.122 AC: 1292 AN: 10614

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.127 AC: 8607 AN: 67908

Other (OTH) AF: 0.168 AC: 352 AN: 2100

Alfa AF: 0.147 Hom.: 1139

Bravo AF: 0.152

Asia WGS AF: 0.312 AC: 1086 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.6
DANN	Benign	0.35
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs16839962; hg19: chr2-156925286;