9-135582939-T-C

Position:

• chr9-135582939-T-C

Variant summary

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

The ENST00000445997.1(LINC01502):​n.337T>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 0.753 in 152,246 control chromosomes in the GnomAD database, including 43,592 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 0.75 (43561 hom., cov: 33)
  • Exomes 𝑓: 0.77 (31 hom.)
• Consequence: LINC01502 ENST00000445997.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.37

Genes affected

LINC01502 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.942 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC01502	NR_034016.1	n.504T>C		non_coding_transcript_exon_variant	5/6
LINC01502	NR_034017.1	n.363T>C		non_coding_transcript_exon_variant	4/5
LINC01502	NR_109814.1	n.305T>C		non_coding_transcript_exon_variant	3/4
LOC105376316	XR_930428.3	n.329+1954A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01502	ENST00000445997.1	n.337T>C		non_coding_transcript_exon_variant	4/5	2
LINC01502	ENST00000447907.5	n.494T>C		non_coding_transcript_exon_variant	5/6	3

Frequencies

GnomAD3 genomes AF: 0.753 AC: 114472 AN: 152016 Hom.: 43507 Cov.: 33

Gnomad AFR AF: 0.809

Gnomad AMI AF: 0.738

Gnomad AMR AF: 0.833

Gnomad ASJ AF: 0.639

Gnomad EAS AF: 0.964

Gnomad SAS AF: 0.716

Gnomad FIN AF: 0.765

Gnomad MID AF: 0.690

Gnomad NFE AF: 0.692

Gnomad OTH AF: 0.748

GnomAD4 exome AF: 0.768 AC: 86 AN: 112 Hom.: 31 Cov.: 0 AF XY: 0.761 AC XY: 67 AN XY: 88

Gnomad4 AFR exome AF: 1.00

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.771

Gnomad4 OTH exome AF: 0.700

GnomAD4 genome AF: 0.753 AC: 114589 AN: 152134 Hom.: 43561 Cov.: 33 AF XY: 0.758 AC XY: 56351 AN XY: 74380

Gnomad4 AFR AF: 0.809

Gnomad4 AMR AF: 0.833

Gnomad4 ASJ AF: 0.639

Gnomad4 EAS AF: 0.964

Gnomad4 SAS AF: 0.715

Gnomad4 FIN AF: 0.765

Gnomad4 NFE AF: 0.692

Gnomad4 OTH AF: 0.752

Alfa AF: 0.705 Hom.: 45827

Bravo AF: 0.764

Asia WGS AF: 0.859 AC: 2985 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	4.6
DANN	Benign	0.24

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4842007; hg19: chr9-138474785;