ENST00000416309.6:n.165-175C>T

Variant names:

• chr9-94177906-G-A
• rs7045890
• ENST00000416309.6:n.165-175C>T

Variant summary

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

The ENST00000416309.6(LINC02603):​n.165-175C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.928 in 152,320 control chromosomes in the GnomAD database, including 65,668 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 0.93 (65668 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: LINC02603 ENST00000416309.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.376
• Publications: 4 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.965 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02603	NR_046163.1	n.188-175C>T		intron_variant	Intron 3 of 3
LINC02603	NR_046165.1	n.129-175C>T		intron_variant	Intron 2 of 2
LINC02603	NR_160773.1	n.256-175C>T		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02603	ENST00000416309.6	n.165-175C>T		intron_variant	Intron 3 of 3	1
LINC02603	ENST00000602602.3	n.159-175C>T		intron_variant	Intron 2 of 2	1
MIRLET7A1HG	ENST00000652769.2	n.2166G>A		non_coding_transcript_exon_variant	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.928 AC: 141239 AN: 152202 Hom.: 65626 Cov.: 32

Gnomad AFR AF: 0.973

Gnomad AMI AF: 0.925

Gnomad AMR AF: 0.901

Gnomad ASJ AF: 0.967

Gnomad EAS AF: 0.807

Gnomad SAS AF: 0.871

Gnomad FIN AF: 0.897

Gnomad MID AF: 0.953

Gnomad NFE AF: 0.923

Gnomad OTH AF: 0.935

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: 0.928 AC: 141335 AN: 152320 Hom.: 65668 Cov.: 32 AF XY: 0.925 AC XY: 68868 AN XY: 74472

African (AFR) AF: 0.973 AC: 40445 AN: 41574

American (AMR) AF: 0.900 AC: 13773 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.967 AC: 3358 AN: 3472

East Asian (EAS) AF: 0.807 AC: 4180 AN: 5182

South Asian (SAS) AF: 0.871 AC: 4207 AN: 4832

European-Finnish (FIN) AF: 0.897 AC: 9513 AN: 10604

Middle Eastern (MID) AF: 0.952 AC: 280 AN: 294

European-Non Finnish (NFE) AF: 0.923 AC: 62766 AN: 68032

Other (OTH) AF: 0.931 AC: 1969 AN: 2116

Alfa AF: 0.929 Hom.: 8170

Bravo AF: 0.930

Asia WGS AF: 0.831 AC: 2889 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.9
DANN	Benign	0.61
PhyloP100		-0.38

Splicing

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

Other links and lift over

dbSNP: rs7045890; hg19: chr9-96940188;