10-70007598-C-A

Variant names:

• chr10-70007598-C-A
• rs2894103
• ENST00000427247.2:n.313G>T

Variant summary

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

The ENST00000427247.2(LINC02636):​n.313G>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 ENST00000427247.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.126
• Publications: 3 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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	ENST00000427247.2	n.313G>T		non_coding_transcript_exon_variant	Exon 3 of 4	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

African (AFR) AF: 0.00 AC: 0 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.500 AC: 1 AN: 2

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.537 AC: 22243 AN: 41422

American (AMR) AF: 0.582 AC: 8886 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.440 AC: 1528 AN: 3470

East Asian (EAS) AF: 0.658 AC: 3403 AN: 5172

South Asian (SAS) AF: 0.623 AC: 2997 AN: 4810

European-Finnish (FIN) AF: 0.406 AC: 4274 AN: 10536

Middle Eastern (MID) AF: 0.497 AC: 146 AN: 294

European-Non Finnish (NFE) AF: 0.460 AC: 31266 AN: 67954

Other (OTH) AF: 0.504 AC: 1064 AN: 2112

Alfa AF: 0.484 Hom.: 9830

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
PhyloP100		0.13

Splicing

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

Other links and lift over

dbSNP: rs2894103; hg19: chr10-71767354;