20-5432077-C-A

Position:

• chr20-5432077-C-A

Variant summary

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

The NR_038240.1(LINC00658):​n.1497G>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 0.248 in 152,218 control chromosomes in the GnomAD database, including 5,178 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 0.25 (5178 hom., cov: 33)
  • Exomes 𝑓: 0.33 (0 hom.)
• Consequence: LINC00658 NR_038240.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.787

Genes affected

LINC00658 (HGNC:44315): (long intergenic non-protein coding RNA 658)

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.3 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC00658	NR_038240.1	n.1497G>T		non_coding_transcript_exon_variant	5/5
LINC00658	NR_038239.1	n.1519G>T		non_coding_transcript_exon_variant	5/5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC00658	ENST00000600157.6	n.1696G>T		non_coding_transcript_exon_variant	11/11	5
	ENST00000668553.1	n.1280+25680C>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.248 AC: 37694 AN: 152086 Hom.: 5176 Cov.: 33

Gnomad AFR AF: 0.148

Gnomad AMI AF: 0.293

Gnomad AMR AF: 0.216

Gnomad ASJ AF: 0.369

Gnomad EAS AF: 0.133

Gnomad SAS AF: 0.210

Gnomad FIN AF: 0.353

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.304

Gnomad OTH AF: 0.254

GnomAD4 exome AF: 0.333 AC: 4 AN: 12 Hom.: 0 Cov.: 0 AF XY: 0.167 AC XY: 1 AN XY: 6

Gnomad4 EAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.375

GnomAD4 genome AF: 0.248 AC: 37702 AN: 152206 Hom.: 5178 Cov.: 33 AF XY: 0.249 AC XY: 18522 AN XY: 74406

Gnomad4 AFR AF: 0.148

Gnomad4 AMR AF: 0.215

Gnomad4 ASJ AF: 0.369

Gnomad4 EAS AF: 0.134

Gnomad4 SAS AF: 0.211

Gnomad4 FIN AF: 0.353

Gnomad4 NFE AF: 0.304

Gnomad4 OTH AF: 0.249

Alfa AF: 0.263 Hom.: 3338

Bravo AF: 0.233

Asia WGS AF: 0.142 AC: 493 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	3.7
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs709028; hg19: chr20-5412723; COSMIC: COSV68976400;