rs2891285

Variant names:

• chr1-187553542-T-C
• rs2891285
• ENST00000643891.1:n.1169-17591T>C

Variant summary

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

The ENST00000643891.1(LINC01036):​n.1169-17591T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0713 in 152,072 control chromosomes in the GnomAD database, including 921 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 0.071 (921 hom., cov: 31)
• Consequence: LINC01036 ENST00000643891.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.31

Genes affected

LINC01036 (HGNC:49024): (long intergenic non-protein coding RNA 1036)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.197 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01036	ENST00000643891.1	n.1169-17591T>C		intron_variant	Intron 6 of 8

Frequencies

GnomAD3 genomes AF: 0.0711 AC: 10802 AN: 151954 Hom.: 913 Cov.: 31

Gnomad AFR AF: 0.200

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.0320

Gnomad ASJ AF: 0.0406

Gnomad EAS AF: 0.0470

Gnomad SAS AF: 0.0882

Gnomad FIN AF: 0.0216

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0133

Gnomad OTH AF: 0.0445

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

GnomAD4 genome AF: 0.0713 AC: 10836 AN: 152072 Hom.: 921 Cov.: 31 AF XY: 0.0713 AC XY: 5302 AN XY: 74344

Gnomad4 AFR AF: 0.200

Gnomad4 AMR AF: 0.0320

Gnomad4 ASJ AF: 0.0406

Gnomad4 EAS AF: 0.0469

Gnomad4 SAS AF: 0.0876

Gnomad4 FIN AF: 0.0216

Gnomad4 NFE AF: 0.0132

Gnomad4 OTH AF: 0.0449

Alfa AF: 0.0222 Hom.: 250

Bravo AF: 0.0761

Asia WGS AF: 0.0700 AC: 244 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.0
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2891285; hg19: chr1-187522674;