rs709028

Variant names:

• chr20-5432077-C-A
• rs709028
• ENST00000420529.6:n.1519G>T

Your query was ambiguous. Multiple possible variants found:

• chr20-5432077-C-A
• chr20-5432077-C-G
• chr20-5432077-C-T

Variant summary

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

The ENST00000420529.6(LINC00658):​n.1519G>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 ENST00000420529.6 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.787
• Publications: 1 publications found

Genes affected

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

ENSG00000230563 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000420529.6. 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
	LINC00658	NR_038239.1		n.1519G>T		non_coding_transcript_exon	Exon 5 of 5
	LINC00658	NR_038240.1		n.1497G>T		non_coding_transcript_exon	Exon 5 of 5

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00658	ENST00000420529.6	TSL:1	n.1519G>T		non_coding_transcript_exon	Exon 6 of 6
	LINC00658	ENST00000414677.2	TSL:2	n.614G>T		non_coding_transcript_exon	Exon 3 of 3
	LINC00658	ENST00000422352.6	TSL:3	n.1204G>T		non_coding_transcript_exon	Exon 5 of 5

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.00 AC: 0 AN: 2

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.500 AC: 1 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.375 AC: 3 AN: 8

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.148 AC: 6156 AN: 41550

American (AMR) AF: 0.215 AC: 3293 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.369 AC: 1280 AN: 3470

East Asian (EAS) AF: 0.134 AC: 695 AN: 5190

South Asian (SAS) AF: 0.211 AC: 1019 AN: 4822

European-Finnish (FIN) AF: 0.353 AC: 3736 AN: 10572

Middle Eastern (MID) AF: 0.303 AC: 89 AN: 294

European-Non Finnish (NFE) AF: 0.304 AC: 20641 AN: 67990

Other (OTH) AF: 0.249 AC: 526 AN: 2110

Alfa AF: 0.273 Hom.: 12169

Bravo AF: 0.233

Asia WGS AF: 0.142 AC: 493 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	3.7
DANN	Benign	0.74
PhyloP100		0.79

Splicing

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

Other links and lift over

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