rs2875991

chr20-5463001-A-Gchr20-5463001-A-T

Variant summary

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

The ENST00000600157.6(LINC00658):n.291+759T>C 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 0.0883 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 ENST00000600157.6 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.58

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=-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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00658	ENST00000600157.6	n.291+759T>C		intron_variant, non_coding_transcript_variant		5
	ENST00000651499.1	n.544-3663A>G		intron_variant, non_coding_transcript_variant
	ENST00000668553.1	n.1281-39546A>G		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.0463

Gnomad4 AMR AF: 0.113

Gnomad4 ASJ AF: 0.180

Gnomad4 EAS AF: 0.0288

Gnomad4 SAS AF: 0.166

Gnomad4 FIN AF: 0.0737

Gnomad4 NFE AF: 0.105

Gnomad4 OTH AF: 0.112

Alfa AF: 0.0935 Hom.: 79

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2875991; hg19: chr20-5443647;