rs2894103

Variant names:

• chr10-70007598-C-A
• rs2894103
• ENST00000427247.1:n.154G>T

Your query was ambiguous. Multiple possible variants found:

• chr10-70007598-C-A
• chr10-70007598-C-G
• chr10-70007598-C-T

Variant summary

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

The ENST00000427247.1(LINC02636):​n.154G>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.501 in 151,950 control chromosomes in the GnomAD database, including 19,428 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 0.50 (19428 hom., cov: 32)
  • Exomes 𝑓: 0.25 (0 hom.)
• Consequence: LINC02636 ENST00000427247.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.126

Genes affected

LINC02636 (HGNC:54119): (long intergenic non-protein coding RNA 2636)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.64 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02636	NR_184064.1	n.1637G>T		non_coding_transcript_exon_variant	Exon 2 of 4
LINC02636	NR_184065.1	n.1637G>T		non_coding_transcript_exon_variant	Exon 2 of 5
LINC02636	NR_184066.1	n.1637G>T		non_coding_transcript_exon_variant	Exon 2 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02636	ENST00000427247.1	n.154G>T		non_coding_transcript_exon_variant	Exon 2 of 3	3
LINC02636	ENST00000653732.1	n.845G>T		non_coding_transcript_exon_variant	Exon 4 of 6
LINC02636	ENST00000655496.1	n.711G>T		non_coding_transcript_exon_variant	Exon 3 of 5

Frequencies

GnomAD3 genomes AF: 0.501 AC: 76109 AN: 151828 Hom.: 19396 Cov.: 32

Gnomad AFR AF: 0.537

Gnomad AMI AF: 0.431

Gnomad AMR AF: 0.582

Gnomad ASJ AF: 0.440

Gnomad EAS AF: 0.659

Gnomad SAS AF: 0.623

Gnomad FIN AF: 0.406

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.460

Gnomad OTH AF: 0.502

GnomAD4 exome AF: 0.250 AC: 1 AN: 4 Hom.: 0 Cov.: 0 AF XY: 0.500 AC XY: 1 AN XY: 2

Gnomad4 AFR exome AF: 0.00

Gnomad4 NFE exome AF: 0.500

GnomAD4 genome AF: 0.501 AC: 76198 AN: 151946 Hom.: 19428 Cov.: 32 AF XY: 0.504 AC XY: 37426 AN XY: 74244

Gnomad4 AFR AF: 0.537

Gnomad4 AMR AF: 0.582

Gnomad4 ASJ AF: 0.440

Gnomad4 EAS AF: 0.658

Gnomad4 SAS AF: 0.623

Gnomad4 FIN AF: 0.406

Gnomad4 NFE AF: 0.460

Gnomad4 OTH AF: 0.504

Alfa AF: 0.486 Hom.: 9024

Bravo AF: 0.515

Asia WGS AF: 0.633 AC: 2201 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.6
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2894103; hg19: chr10-71767354;