20-5447654-C-T

Variant summary

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

The ENST00000600157.6(LINC00658):n.342+1010G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0414 in 152,158 control chromosomes in the GnomAD database, including 183 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 0.041 (183 hom., cov: 33)
• Consequence: LINC00658 ENST00000600157.6 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0900

Genes affected

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

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.14 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00658	ENST00000600157.6	n.342+1010G>A		intron_variant, non_coding_transcript_variant		5
	ENST00000651499.1	n.427+1390C>T		intron_variant, non_coding_transcript_variant
	ENST00000668553.1	n.1280+41257C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0414 AC: 6294 AN: 152040 Hom.: 185 Cov.: 33

Gnomad AFR AF: 0.0262

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.0524

Gnomad ASJ AF: 0.0625

Gnomad EAS AF: 0.0277

Gnomad SAS AF: 0.150

Gnomad FIN AF: 0.0440

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0401

Gnomad OTH AF: 0.0474

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

GnomAD4 genome AF: 0.0414 AC: 6296 AN: 152158 Hom.: 183 Cov.: 33 AF XY: 0.0438 AC XY: 3259 AN XY: 74384

Gnomad4 AFR AF: 0.0263

Gnomad4 AMR AF: 0.0524

Gnomad4 ASJ AF: 0.0625

Gnomad4 EAS AF: 0.0278

Gnomad4 SAS AF: 0.150

Gnomad4 FIN AF: 0.0440

Gnomad4 NFE AF: 0.0401

Gnomad4 OTH AF: 0.0469

Alfa AF: 0.0244 Hom.: 35

Bravo AF: 0.0380

Asia WGS AF: 0.0850 AC: 299 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	0.87
Dann	Benign	0.20

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10485489; hg19: chr20-5428300;