20-5463001-A-G

Variant names:

• chr20-5463001-A-G
• rs2875991
• ENST00000593667.2:n.317+759T>C

Variant summary

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

The ENST00000593667.2(LINC00658):​n.317+759T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0883 in 152,242 control chromosomes in the GnomAD database, including 757 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 0.088 (757 hom., cov: 32)
• Consequence: LINC00658 ENST00000593667.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.58
• 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=-1.02).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.156 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00658	ENST00000593667.2	n.317+759T>C		intron_variant	Intron 3 of 5	6
LINC00658	ENST00000600157.6	n.291+759T>C		intron_variant	Intron 3 of 10	5
ENSG00000230563	ENST00000651499.1	n.544-3663A>G		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.0883 AC: 13435 AN: 152124 Hom.: 757 Cov.: 32

Gnomad AFR AF: 0.0463

Gnomad AMI AF: 0.0285

Gnomad AMR AF: 0.113

Gnomad ASJ AF: 0.180

Gnomad EAS AF: 0.0287

Gnomad SAS AF: 0.166

Gnomad FIN AF: 0.0737

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.105

Gnomad OTH AF: 0.113

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

GnomAD4 genome AF: 0.0883 AC: 13436 AN: 152242 Hom.: 757 Cov.: 32 AF XY: 0.0892 AC XY: 6639 AN XY: 74442

African (AFR) AF: 0.0463 AC: 1925 AN: 41538

American (AMR) AF: 0.113 AC: 1721 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.180 AC: 624 AN: 3470

East Asian (EAS) AF: 0.0288 AC: 149 AN: 5176

South Asian (SAS) AF: 0.166 AC: 801 AN: 4826

European-Finnish (FIN) AF: 0.0737 AC: 781 AN: 10598

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.105 AC: 7128 AN: 68016

Other (OTH) AF: 0.112 AC: 237 AN: 2116

Alfa AF: 0.0909 Hom.: 80

Bravo AF: 0.0865

Asia WGS AF: 0.0980 AC: 343 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.32
PhyloP100		-2.6

Splicing

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

Other links and lift over

dbSNP: rs2875991; hg19: chr20-5443647;