rs10492680

chr13-40230699-A-G

Variant summary

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

The ENST00000615947.1(LINC00598):n.47-12949T>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 0.301 in 151,994 control chromosomes in the GnomAD database, including 7,656 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 0.30 (7656 hom., cov: 31)
• Consequence: LINC00598 ENST00000615947.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.95

Genes affected

LINC00598 (HGNC:42770): (long intergenic non-protein coding RNA 598)

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 = 0.449 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
LINC00598	ENST00000615947.1	n.47-12949T>C		intron_variant, non_coding_transcript_variant		4
LINC00598	ENST00000637438.1	n.401-23647T>C		intron_variant, non_coding_transcript_variant		5
LINC00598	ENST00000638084.1	n.406-12949T>C		intron_variant, non_coding_transcript_variant		5
LINC00598	ENST00000654662.1	n.553-29808T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.301 AC: 45762 AN: 151876 Hom.: 7660 Cov.: 31

Gnomad AFR AF: 0.170

Gnomad AMI AF: 0.302

Gnomad AMR AF: 0.298

Gnomad ASJ AF: 0.273

Gnomad EAS AF: 0.104

Gnomad SAS AF: 0.466

Gnomad FIN AF: 0.372

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.376

Gnomad OTH AF: 0.277

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

GnomAD4 genome AF: 0.301 AC: 45764 AN: 151994 Hom.: 7656 Cov.: 31 AF XY: 0.302 AC XY: 22411 AN XY: 74312

Gnomad4 AFR AF: 0.170

Gnomad4 AMR AF: 0.298

Gnomad4 ASJ AF: 0.273

Gnomad4 EAS AF: 0.104

Gnomad4 SAS AF: 0.465

Gnomad4 FIN AF: 0.372

Gnomad4 NFE AF: 0.376

Gnomad4 OTH AF: 0.273

Alfa AF: 0.354 Hom.: 13429

Bravo AF: 0.284

Asia WGS AF: 0.253 AC: 882 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	0.10
Dann	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10492680; hg19: chr13-40804836;