ENST00000794115.1:n.504G>A

Variant names:

• chr20-5447848-G-A
• rs10485490
• ENST00000794115.1:n.504G>A

Variant summary

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

The ENST00000794115.1(ENSG00000230563):​n.504G>A 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 0.0518 in 152,278 control chromosomes in the GnomAD database, including 255 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 0.052 (255 hom., cov: 33)
• Consequence: ENSG00000230563 ENST00000794115.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.174
• Publications: 0 publications found

Genes affected

ENSG00000230563 (HGNC:):

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0628 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000794115.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000230563	ENST00000794115.1		n.504G>A		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000230563	ENST00000794116.1		n.567G>A		non_coding_transcript_exon	Exon 2 of 2
	LINC00658	ENST00000593667.2	TSL:6	n.318-13447C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0519 AC: 7891 AN: 152160 Hom.: 255 Cov.: 33

Gnomad AFR AF: 0.0380

Gnomad AMI AF: 0.0241

Gnomad AMR AF: 0.0621

Gnomad ASJ AF: 0.117

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0176

Gnomad FIN AF: 0.0290

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.0644

Gnomad OTH AF: 0.0684

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0518 AC: 7889 AN: 152278 Hom.: 255 Cov.: 33 AF XY: 0.0502 AC XY: 3742 AN XY: 74480

African (AFR) AF: 0.0379 AC: 1573 AN: 41542

American (AMR) AF: 0.0620 AC: 948 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.117 AC: 407 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5190

South Asian (SAS) AF: 0.0180 AC: 87 AN: 4826

European-Finnish (FIN) AF: 0.0290 AC: 308 AN: 10616

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.0644 AC: 4379 AN: 68020

Other (OTH) AF: 0.0676 AC: 143 AN: 2114

Alfa AF: 0.0585 Hom.: 155

Bravo AF: 0.0546

Asia WGS AF: 0.00837 AC: 29 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.6
DANN	Benign	0.71
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs10485490; hg19: chr20-5428494;