9-135582939-T-C

Variant names:

• chr9-135582939-T-C
• rs4842007
• ENST00000445997.1:n.337T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

Genes affected

LINC01502 (HGNC:51183): (long intergenic non-protein coding RNA 1502)

ENSG00000300457 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000445997.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01502	NR_034016.1		n.504T>C		non_coding_transcript_exon	Exon 5 of 6
	LINC01502	NR_034017.1		n.363T>C		non_coding_transcript_exon	Exon 4 of 5
	LINC01502	NR_109814.1		n.305T>C		non_coding_transcript_exon	Exon 3 of 4

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01502	ENST00000445997.1	TSL:2	n.337T>C		non_coding_transcript_exon	Exon 4 of 5
	LINC01502	ENST00000447907.5	TSL:3	n.494T>C		non_coding_transcript_exon	Exon 5 of 6
	ENSG00000300457	ENST00000771890.1		n.311+1954A>G		intron	N/A

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

African (AFR) AF: 1.00 AC: 4 AN: 4

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) AF: 0.500 AC: 1 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.771 AC: 74 AN: 96

Other (OTH) AF: 0.700 AC: 7 AN: 10

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

African (AFR) AF: 0.809 AC: 33576 AN: 41494

American (AMR) AF: 0.833 AC: 12735 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.639 AC: 2215 AN: 3466

East Asian (EAS) AF: 0.964 AC: 4993 AN: 5180

South Asian (SAS) AF: 0.715 AC: 3453 AN: 4826

European-Finnish (FIN) AF: 0.765 AC: 8097 AN: 10590

Middle Eastern (MID) AF: 0.684 AC: 201 AN: 294

European-Non Finnish (NFE) AF: 0.692 AC: 47063 AN: 67976

Other (OTH) AF: 0.752 AC: 1583 AN: 2104

Alfa AF: 0.711 Hom.: 57702

Bravo AF: 0.764

Asia WGS AF: 0.859 AC: 2985 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	4.6
DANN	Benign	0.24
PhyloP100		-2.4

Splicing

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

Other links and lift over

dbSNP: rs4842007; hg19: chr9-138474785;