rs708629

Positions:

• chr20-62775532-A-G

Variant summary

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

The ENST00000412500.2(LINC00659):​n.171T>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 0.317 in 151,996 control chromosomes in the GnomAD database, including 11,479 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 0.32 (11478 hom., cov: 32)
  • Exomes 𝑓: 0.13 (1 hom.)
• Consequence: LINC00659 ENST00000412500.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.03

Genes affected

LINC00659 (HGNC:44316): (long intergenic non-protein coding RNA 659)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.652 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC00659	NR_046225.1	n.52-146T>C		intron_variant, non_coding_transcript_variant
LINC00659	NR_046224.1	n.52-12T>C		splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00659	ENST00000689171.1	n.152-53T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.316 AC: 48022 AN: 151826 Hom.: 11428 Cov.: 32

Gnomad AFR AF: 0.658

Gnomad AMI AF: 0.0956

Gnomad AMR AF: 0.268

Gnomad ASJ AF: 0.181

Gnomad EAS AF: 0.466

Gnomad SAS AF: 0.363

Gnomad FIN AF: 0.174

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.139

Gnomad OTH AF: 0.285

GnomAD4 exome AF: 0.135 AC: 7 AN: 52 Hom.: 1 AF XY: 0.167 AC XY: 5 AN XY: 30

Gnomad4 AFR exome AF: 0.500

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.143

Gnomad4 NFE exome AF: 0.125

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.317 AC: 48129 AN: 151944 Hom.: 11478 Cov.: 32 AF XY: 0.318 AC XY: 23631 AN XY: 74264

Gnomad4 AFR AF: 0.658

Gnomad4 AMR AF: 0.268

Gnomad4 ASJ AF: 0.181

Gnomad4 EAS AF: 0.466

Gnomad4 SAS AF: 0.361

Gnomad4 FIN AF: 0.174

Gnomad4 NFE AF: 0.139

Gnomad4 OTH AF: 0.291

Alfa AF: 0.201 Hom.: 3005

Bravo AF: 0.339

Asia WGS AF: 0.432 AC: 1499 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.5
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs708629; hg19: chr20-61406884;