rs15680

Variant names:

• chr6-57946158-C-A
• rs15680
• ENST00000399751.7:n.1589G>T

Your query was ambiguous. Multiple possible variants found:

• chr6-57946158-C-A
• chr6-57946158-C-G
• chr6-57946158-C-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000399751.7(LINC00680):​n.1589G>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 0.00000659 in 151,804 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.0000066 (0 hom., cov: 30)
• Consequence: LINC00680 ENST00000399751.7 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0760
• Publications: 3 publications found

Genes affected

LINC00680 (HGNC:):

LINC00680 (HGNC:44417): (long intergenic non-protein coding RNA 680)

LINC00680-GUSBP4 (HGNC:56755): (LINC00680-GUSBP4 readthrough, transcribed pseudogene) This locus represents naturally-occurring readthrough transcription between the neighboring LINC00680 (long intergenic non-protein coding RNA 680) and GUSBP4 (glucuronidase, beta pseudogene 4) genes on chromosome 6. The readthrough transcript is unlikely to encode a protein. [provided by RefSeq, Oct 2015]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000399751.7. 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
	LINC00680	NR_125727.1		n.1652G>T		non_coding_transcript_exon	Exon 6 of 6
	LINC00680	NR_125728.1		n.1499G>T		non_coding_transcript_exon	Exon 5 of 5
	LINC00680	NR_125729.1		n.1454G>T		non_coding_transcript_exon	Exon 5 of 5

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00680	ENST00000399751.7	TSL:1	n.1589G>T		non_coding_transcript_exon	Exon 6 of 6
	LINC00680	ENST00000450081.6	TSL:1	n.1509G>T		non_coding_transcript_exon	Exon 5 of 5
	LINC00680	ENST00000418368.2	TSL:2	n.1649G>T		non_coding_transcript_exon	Exon 6 of 6

Frequencies

GnomAD3 genomes AF: 0.00000659 AC: 1 AN: 151804 Hom.: 0 Cov.: 30

Gnomad AFR AF: 0.0000242

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD4 exome Cov.: 0

GnomAD4 genome AF: 0.00000659 AC: 1 AN: 151804 Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0 AN XY: 74118

African (AFR) AF: 0.0000242 AC: 1 AN: 41298

American (AMR) AF: 0.00 AC: 0 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5170

South Asian (SAS) AF: 0.00 AC: 0 AN: 4818

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10540

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 316

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 67958

Other (OTH) AF: 0.00 AC: 0 AN: 2092

Alfa AF: 0.00 Hom.: 1668

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.5
DANN	Benign	0.47
PhyloP100		0.076

Splicing

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

Other links and lift over

dbSNP: rs15680; hg19: chr6-58272436;