rs10504337

Variant names:

• chr8-61852708-T-C
• rs10504337
• ENST00000517953.6:n.279T>C

Variant summary

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

The ENST00000517953.6(LINC02842):​n.279T>C 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 0.0218 in 152,296 control chromosomes in the GnomAD database, including 127 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 0.022 (127 hom., cov: 33)
  • Failed GnomAD Quality Control
• Consequence: LINC02842 ENST00000517953.6 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0130
• Publications: 0 publications found

Genes affected

LINC02842 (HGNC:54378): (long intergenic non-protein coding RNA 2842)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0997 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02842	NR_187553.1	n.479T>C		non_coding_transcript_exon_variant	Exon 4 of 5
LINC02842	NR_187554.1	n.479T>C		non_coding_transcript_exon_variant	Exon 4 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02842	ENST00000517953.6	n.279T>C		non_coding_transcript_exon_variant	Exon 3 of 5	3
LINC02842	ENST00000518593.5	n.359T>C		non_coding_transcript_exon_variant	Exon 3 of 4	3
LINC02842	ENST00000519452.6	n.395T>C		non_coding_transcript_exon_variant	Exon 3 of 4	3

Frequencies

GnomAD3 genomes AF: 0.0218 AC: 3312 AN: 152180 Hom.: 125 Cov.: 33

Gnomad AFR AF: 0.00323

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.104

Gnomad ASJ AF: 0.00980

Gnomad EAS AF: 0.00115

Gnomad SAS AF: 0.0194

Gnomad FIN AF: 0.0322

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.0158

Gnomad OTH AF: 0.0186

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

African (AFR) AC: 0 AN: 0

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) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.0218 AC: 3318 AN: 152296 Hom.: 127 Cov.: 33 AF XY: 0.0248 AC XY: 1850 AN XY: 74462

African (AFR) AF: 0.00322 AC: 134 AN: 41586

American (AMR) AF: 0.104 AC: 1589 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.00980 AC: 34 AN: 3470

East Asian (EAS) AF: 0.00116 AC: 6 AN: 5184

South Asian (SAS) AF: 0.0197 AC: 95 AN: 4830

European-Finnish (FIN) AF: 0.0322 AC: 342 AN: 10620

Middle Eastern (MID) AF: 0.00340 AC: 1 AN: 294

European-Non Finnish (NFE) AF: 0.0158 AC: 1074 AN: 67994

Other (OTH) AF: 0.0184 AC: 39 AN: 2114

Alfa AF: 0.0157 Hom.: 35

Bravo AF: 0.0254

Asia WGS AF: 0.0120 AC: 40 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.3
DANN	Benign	0.86
PhyloP100		-0.013

Splicing

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

Other links and lift over

dbSNP: rs10504337; hg19: chr8-62765267;