rs17090302

Variant names:

• chr13-73587739-A-G
• rs17090302
• ENST00000430033.1:n.226A>G

Variant summary

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

The ENST00000430033.1(LINC00392):​n.226A>G 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 0.0675 in 152,268 control chromosomes in the GnomAD database, including 451 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 0.068 (451 hom., cov: 33)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: LINC00392 ENST00000430033.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0620
• Publications: 2 publications found

Genes affected

LINC00392 (HGNC:42720): (long intergenic non-protein coding RNA 392)

LINC00393 (HGNC:42721): (long intergenic non-protein coding RNA 393)

LOC128966561 (HGNC:):

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 (SAS) allele frequency at 95% confidence interval = 0.129 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00392	NR_047009.1	n.226A>G		non_coding_transcript_exon_variant	Exon 3 of 3
LINC00393	NR_184171.1	n.143-40898T>C		intron_variant	Intron 2 of 3
LOC128966561	XR_001749905.2	n.281+5529T>C		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00392	ENST00000430033.1	n.226A>G		non_coding_transcript_exon_variant	Exon 3 of 3	3
LINC00392	ENST00000660666.1	n.598A>G		non_coding_transcript_exon_variant	Exon 3 of 3
LINC00392	ENST00000666930.1	n.482A>G		non_coding_transcript_exon_variant	Exon 3 of 3

Frequencies

GnomAD3 genomes AF: 0.0674 AC: 10254 AN: 152150 Hom.: 449 Cov.: 33

Gnomad AFR AF: 0.107

Gnomad AMI AF: 0.0724

Gnomad AMR AF: 0.0802

Gnomad ASJ AF: 0.0622

Gnomad EAS AF: 0.0508

Gnomad SAS AF: 0.136

Gnomad FIN AF: 0.0480

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0403

Gnomad OTH AF: 0.0599

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 34 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 28

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) AF: 0.00 AC: 0 AN: 2

South Asian (SAS) AC: 0 AN: 0

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

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 26

Other (OTH) AF: 0.00 AC: 0 AN: 2

GnomAD4 genome AF: 0.0675 AC: 10279 AN: 152268 Hom.: 451 Cov.: 33 AF XY: 0.0701 AC XY: 5219 AN XY: 74456

African (AFR) AF: 0.107 AC: 4447 AN: 41544

American (AMR) AF: 0.0806 AC: 1233 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0622 AC: 216 AN: 3470

East Asian (EAS) AF: 0.0505 AC: 262 AN: 5184

South Asian (SAS) AF: 0.137 AC: 661 AN: 4818

European-Finnish (FIN) AF: 0.0480 AC: 510 AN: 10626

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.0402 AC: 2737 AN: 68014

Other (OTH) AF: 0.0592 AC: 125 AN: 2110

Alfa AF: 0.0496 Hom.: 400

Bravo AF: 0.0699

Asia WGS AF: 0.0950 AC: 331 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.4
DANN	Benign	0.85
PhyloP100		0.062
Mutation Taster		=99/1	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs17090302; hg19: chr13-74161876;