rs1356743

Variant names:

• chr2-156199390-C-T
• rs1356743
• ENST00000428651.2:n.159+55388G>A

Variant summary

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

The ENST00000428651.2(LINC01876):​n.159+55388G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.465 in 151,852 control chromosomes in the GnomAD database, including 19,180 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 0.46 (19180 hom., cov: 32)
• Consequence: LINC01876 ENST00000428651.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.643
• 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=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.76 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01876	NR_110249.2	n.154+55388G>A		intron_variant	Intron 1 of 3
LINC01876	NR_110250.2	n.154+55388G>A		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01876	ENST00000428651.2	n.159+55388G>A		intron_variant	Intron 1 of 3	5
LINC01876	ENST00000635799.1	n.152+55388G>A		intron_variant	Intron 1 of 4	5
LINC01876	ENST00000636956.1	n.268+5992G>A		intron_variant	Intron 3 of 5	5

Frequencies

GnomAD3 genomes AF: 0.465 AC: 70496 AN: 151734 Hom.: 19120 Cov.: 32

Gnomad AFR AF: 0.767

Gnomad AMI AF: 0.241

Gnomad AMR AF: 0.343

Gnomad ASJ AF: 0.471

Gnomad EAS AF: 0.343

Gnomad SAS AF: 0.389

Gnomad FIN AF: 0.331

Gnomad MID AF: 0.334

Gnomad NFE AF: 0.347

Gnomad OTH AF: 0.430

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

GnomAD4 genome AF: 0.465 AC: 70611 AN: 151852 Hom.: 19180 Cov.: 32 AF XY: 0.462 AC XY: 34242 AN XY: 74182

African (AFR) AF: 0.767 AC: 31820 AN: 41470

American (AMR) AF: 0.343 AC: 5219 AN: 15214

Ashkenazi Jewish (ASJ) AF: 0.471 AC: 1632 AN: 3466

East Asian (EAS) AF: 0.343 AC: 1771 AN: 5164

South Asian (SAS) AF: 0.390 AC: 1879 AN: 4818

European-Finnish (FIN) AF: 0.331 AC: 3472 AN: 10494

Middle Eastern (MID) AF: 0.322 AC: 94 AN: 292

European-Non Finnish (NFE) AF: 0.347 AC: 23597 AN: 67920

Other (OTH) AF: 0.431 AC: 908 AN: 2106

Alfa AF: 0.430 Hom.: 2589

Bravo AF: 0.479

Asia WGS AF: 0.402 AC: 1401 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	5.7
DANN	Benign	0.67
PhyloP100		0.64

Splicing

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

Other links and lift over

dbSNP: rs1356743; hg19: chr2-157055902;