20-5448343-T-C

Variant names:

• chr20-5448343-T-C
• rs10485492
• ENST00000600157.6:n.342+321A>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000600157.6(LINC00658):​n.342+321A>G variant causes a intron 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: LINC00658 ENST00000600157.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.98

Genes affected

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

ENSG00000230563 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

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	ENST00000600157.6	n.342+321A>G		intron_variant	Intron 4 of 10	5
ENSG00000230563	ENST00000651499.1	n.427+2079T>C		intron_variant	Intron 1 of 3
ENSG00000266908	ENST00000668553.1	n.1280+41946T>C		intron_variant	Intron 3 of 3

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

Gnomad4 AFR AF: 0.0124

Gnomad4 AMR AF: 0.0590

Gnomad4 ASJ AF: 0.117

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.0172

Gnomad4 FIN AF: 0.0285

Gnomad4 NFE AF: 0.0642

Gnomad4 OTH AF: 0.0626

Alfa AF: 0.0488 Hom.: 120

Bravo AF: 0.0461

Asia WGS AF: 0.00693 AC: 24 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10485492; hg19: chr20-5428989;