rs708629

Variant names:

• chr20-62775532-A-G
• rs708629
• ENST00000412500.3:n.1423T>C

Variant summary

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

The ENST00000412500.3(LINC00659):​n.1423T>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 ENST00000412500.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.03
• Publications: 8 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LINC00659	NR_046224.1	n.52-12T>C		intron_variant	Intron 1 of 2
LINC00659	NR_046225.1	n.52-146T>C		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00659	ENST00000412500.3	n.1423T>C		non_coding_transcript_exon_variant	Exon 1 of 2	1
LINC00659	ENST00000764060.1	n.1326T>C		non_coding_transcript_exon_variant	Exon 1 of 2
LINC00659	ENST00000653007.2	n.141-12T>C		intron_variant	Intron 1 of 2

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

African (AFR) AF: 0.500 AC: 1 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AF: 0.00 AC: 0 AN: 2

European-Finnish (FIN) AF: 0.143 AC: 2 AN: 14

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.125 AC: 4 AN: 32

Other (OTH) AF: 0.00 AC: 0 AN: 2

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

African (AFR) AF: 0.658 AC: 27250 AN: 41406

American (AMR) AF: 0.268 AC: 4097 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.181 AC: 627 AN: 3468

East Asian (EAS) AF: 0.466 AC: 2379 AN: 5104

South Asian (SAS) AF: 0.361 AC: 1738 AN: 4818

European-Finnish (FIN) AF: 0.174 AC: 1839 AN: 10576

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.139 AC: 9435 AN: 67988

Other (OTH) AF: 0.291 AC: 614 AN: 2108

Alfa AF: 0.191 Hom.: 3740

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
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs708629; hg19: chr20-61406884;