20-5448343-T-C

Variant names:

• chr20-5448343-T-C
• rs10485492
• ENST00000794115.1:n.999T>C

Variant summary

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

The ENST00000794115.1(ENSG00000230563):​n.999T>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 0.0444 in 152,222 control chromosomes in the GnomAD database, including 231 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 0.044 (231 hom., cov: 33)
• Consequence: ENSG00000230563 ENST00000794115.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.98
• Publications: 2 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=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0626 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000230563	ENST00000794115.1		n.999T>C		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000230563	ENST00000794116.1		n.1062T>C		non_coding_transcript_exon	Exon 2 of 2
	LINC00658	ENST00000593667.2	TSL:6	n.318-13942A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0444 AC: 6758 AN: 152110 Hom.: 232 Cov.: 33

Gnomad AFR AF: 0.0125

Gnomad AMI AF: 0.0242

Gnomad AMR AF: 0.0590

Gnomad ASJ AF: 0.117

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0168

Gnomad FIN AF: 0.0285

Gnomad MID AF: 0.0769

Gnomad NFE AF: 0.0643

Gnomad OTH AF: 0.0632

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

GnomAD4 genome AF: 0.0444 AC: 6755 AN: 152222 Hom.: 231 Cov.: 33 AF XY: 0.0427 AC XY: 3179 AN XY: 74420

African (AFR) AF: 0.0124 AC: 517 AN: 41528

American (AMR) AF: 0.0590 AC: 902 AN: 15300

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

East Asian (EAS) AF: 0.00 AC: 0 AN: 5192

South Asian (SAS) AF: 0.0172 AC: 83 AN: 4824

European-Finnish (FIN) AF: 0.0285 AC: 302 AN: 10582

Middle Eastern (MID) AF: 0.0729 AC: 21 AN: 288

European-Non Finnish (NFE) AF: 0.0642 AC: 4369 AN: 68018

Other (OTH) AF: 0.0626 AC: 132 AN: 2110

Alfa AF: 0.0450 Hom.: 174

Bravo AF: 0.0461

Asia WGS AF: 0.00693 AC: 24 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.25
DANN	Benign	0.70
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs10485492; hg19: chr20-5428989;