6-30806580-G-A

Variant names:

• chr6-30806580-G-A
• rs3130783
• ENST00000719501.1:n.453C>T

Variant summary

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

The ENST00000719501.1(LINC00243):​n.453C>T 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 0.75 in 151,084 control chromosomes in the GnomAD database, including 43,119 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as not provided (no stars).

• Frequency: Genomes: 𝑓 0.75 (43119 hom., cov: 28)
• Consequence: LINC00243 ENST00000719501.1 non_coding_transcript_exon
• Clinical Significance: not provided no classification provided O:1
• Conservation: PhyloP100: -0.630
• Publications: 42 publications found

Genes affected

LINC00243 (HGNC:30956): (long intergenic non-protein coding RNA 243)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.885 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00243	ENST00000719501.1	n.453C>T		non_coding_transcript_exon_variant	Exon 1 of 1
LINC00243	ENST00000419357.7	n.146-7808C>T		intron_variant	Intron 1 of 1	3
LINC00243	ENST00000719489.1	n.498-7808C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.750 AC: 113179 AN: 150968 Hom.: 43086 Cov.: 28

Gnomad AFR AF: 0.611

Gnomad AMI AF: 0.896

Gnomad AMR AF: 0.741

Gnomad ASJ AF: 0.821

Gnomad EAS AF: 0.836

Gnomad SAS AF: 0.908

Gnomad FIN AF: 0.870

Gnomad MID AF: 0.782

Gnomad NFE AF: 0.795

Gnomad OTH AF: 0.736

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.750 AC: 113267 AN: 151084 Hom.: 43119 Cov.: 28 AF XY: 0.755 AC XY: 55702 AN XY: 73756

African (AFR) AF: 0.611 AC: 25179 AN: 41218

American (AMR) AF: 0.741 AC: 11184 AN: 15096

Ashkenazi Jewish (ASJ) AF: 0.821 AC: 2840 AN: 3458

East Asian (EAS) AF: 0.837 AC: 4295 AN: 5134

South Asian (SAS) AF: 0.908 AC: 4327 AN: 4766

European-Finnish (FIN) AF: 0.870 AC: 9008 AN: 10356

Middle Eastern (MID) AF: 0.779 AC: 229 AN: 294

European-Non Finnish (NFE) AF: 0.795 AC: 53843 AN: 67756

Other (OTH) AF: 0.738 AC: 1548 AN: 2098

Alfa AF: 0.749 Hom.: 42219

Bravo AF: 0.733

Asia WGS AF: 0.865 AC: 3008 AN: 3476

ClinVar

Significance: not provided

Submissions summary: Other:1

Revision: no classification provided

Submissions by phenotype

not provided Other:1

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Department of Ophthalmology and Visual Sciences Kyoto University

Significance: not provided

Review Status: no classification provided

Collection Method: not provided

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.3
DANN	Benign	0.26
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs3130783; hg19: chr6-30774357;