6-57946158-C-G

Position:

• chr6-57946158-C-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_132996.1(LINC00680):​n.1426G>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 NR_132996.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0760

Genes affected

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

LINC00680-GUSBP4 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC00680	NR_132996.1	n.1426G>C		non_coding_transcript_exon_variant	4/4
LINC00680-GUSBP4	NR_132998.1	n.210+12870G>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00680	ENST00000399751.6	n.1541G>C		non_coding_transcript_exon_variant	6/6	1
LINC00680	ENST00000450081.5	n.1509G>C		non_coding_transcript_exon_variant	5/5	1
LINC00680	ENST00000418368.1	n.1586G>C		non_coding_transcript_exon_variant	6/6	2
LINC00680	ENST00000422882.1	n.2547G>C		non_coding_transcript_exon_variant	2/2	2

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

Gnomad4 NFE exome AF: 0.500

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

Gnomad4 AFR AF: 0.523

Gnomad4 AMR AF: 0.764

Gnomad4 ASJ AF: 0.738

Gnomad4 EAS AF: 0.593

Gnomad4 SAS AF: 0.717

Gnomad4 FIN AF: 0.701

Gnomad4 NFE AF: 0.699

Gnomad4 OTH AF: 0.691

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs15680; hg19: chr6-58272436;