9-94177436-A-G

Variant names:

• chr9-94177436-A-G
• rs10993081
• ENST00000416309.6:n.460T>C

Variant summary

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

The ENST00000416309.6(LINC02603):​n.460T>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 0.0634 in 152,290 control chromosomes in the GnomAD database, including 513 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 0.063 (513 hom., cov: 33)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: LINC02603 ENST00000416309.6 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.300
• Publications: 6 publications found

Genes affected

LINC02603 (HGNC:37186): (long intergenic non-protein coding RNA 2603)

MIRLET7A1HG (HGNC:53970): (miRlet-7a-1/let-7f-1/let-7d cluster host gene)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.205 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000416309.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02603	NR_046163.1		n.483T>C		non_coding_transcript_exon	Exon 4 of 4
	LINC02603	NR_046165.1		n.424T>C		non_coding_transcript_exon	Exon 3 of 3
	LINC02603	NR_160773.1		n.551T>C		non_coding_transcript_exon	Exon 3 of 3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02603	ENST00000416309.6	TSL:1	n.460T>C		non_coding_transcript_exon	Exon 4 of 4
	LINC02603	ENST00000602602.3	TSL:1	n.454T>C		non_coding_transcript_exon	Exon 3 of 3
	LINC02603	ENST00000602652.3	TSL:6	n.704T>C		non_coding_transcript_exon	Exon 4 of 4

Frequencies

GnomAD3 genomes AF: 0.0635 AC: 9667 AN: 152172 Hom.: 517 Cov.: 33

Gnomad AFR AF: 0.0140

Gnomad AMI AF: 0.0482

Gnomad AMR AF: 0.149

Gnomad ASJ AF: 0.0726

Gnomad EAS AF: 0.216

Gnomad SAS AF: 0.0990

Gnomad FIN AF: 0.0465

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.0623

Gnomad OTH AF: 0.0737

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 4 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 2

African (AFR) AF: 0.00 AC: 0 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) 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: 0.0634 AC: 9653 AN: 152290 Hom.: 513 Cov.: 33 AF XY: 0.0657 AC XY: 4895 AN XY: 74462

African (AFR) AF: 0.0140 AC: 580 AN: 41576

American (AMR) AF: 0.149 AC: 2273 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0726 AC: 252 AN: 3470

East Asian (EAS) AF: 0.215 AC: 1114 AN: 5178

South Asian (SAS) AF: 0.0986 AC: 475 AN: 4816

European-Finnish (FIN) AF: 0.0465 AC: 493 AN: 10606

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.0623 AC: 4240 AN: 68034

Other (OTH) AF: 0.0724 AC: 153 AN: 2112

Alfa AF: 0.0689 Hom.: 1331

Bravo AF: 0.0706

Asia WGS AF: 0.122 AC: 423 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.1
DANN	Benign	0.78
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs10993081; hg19: chr9-96939718;