6-57946158-C-G

Variant names:

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

Variant summary

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

The ENST00000399751.7(LINC00680):​n.1589G>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 0.655 in 151,726 control chromosomes in the GnomAD database, including 33,136 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 0.65 (33136 hom., cov: 30)
  • Exomes 𝑓: 0.50 (0 hom.)
• 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.752 is higher than 0.05.

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>C		non_coding_transcript_exon	Exon 6 of 6
	LINC00680	NR_125728.1		n.1499G>C		non_coding_transcript_exon	Exon 5 of 5
	LINC00680	NR_125729.1		n.1454G>C		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>C		non_coding_transcript_exon	Exon 6 of 6
	LINC00680	ENST00000450081.6	TSL:1	n.1509G>C		non_coding_transcript_exon	Exon 5 of 5
	LINC00680	ENST00000418368.2	TSL:2	n.1649G>C		non_coding_transcript_exon	Exon 6 of 6

Frequencies

GnomAD3 genomes AF: 0.655 AC: 99291 AN: 151608 Hom.: 33127 Cov.: 30

Gnomad AFR AF: 0.524

Gnomad AMI AF: 0.544

Gnomad AMR AF: 0.764

Gnomad ASJ AF: 0.738

Gnomad EAS AF: 0.593

Gnomad SAS AF: 0.717

Gnomad FIN AF: 0.701

Gnomad MID AF: 0.712

Gnomad NFE AF: 0.699

Gnomad OTH AF: 0.696

GnomAD4 exome AF: 0.500 AC: 1 AN: 2 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) AF: 0.500 AC: 1 AN: 2

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.655 AC: 99337 AN: 151724 Hom.: 33136 Cov.: 30 AF XY: 0.655 AC XY: 48582 AN XY: 74152

African (AFR) AF: 0.523 AC: 21629 AN: 41326

American (AMR) AF: 0.764 AC: 11626 AN: 15220

Ashkenazi Jewish (ASJ) AF: 0.738 AC: 2562 AN: 3470

East Asian (EAS) AF: 0.593 AC: 3057 AN: 5152

South Asian (SAS) AF: 0.717 AC: 3447 AN: 4806

European-Finnish (FIN) AF: 0.701 AC: 7377 AN: 10526

Middle Eastern (MID) AF: 0.718 AC: 211 AN: 294

European-Non Finnish (NFE) AF: 0.699 AC: 47477 AN: 67912

Other (OTH) AF: 0.691 AC: 1457 AN: 2110

Alfa AF: 0.575 Hom.: 1668

Bravo AF: 0.653

Asia WGS AF: 0.585 AC: 2033 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.5
DANN	Benign	0.39
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;