rs9566498

chr13-40199515-T-Cchr13-40199515-T-G

Variant summary

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

The XM_047430821.1(LOC124903162):c.53+18063A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.13 in 151,938 control chromosomes in the GnomAD database, including 1,500 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 0.13 (1500 hom., cov: 31)
• Consequence: LOC124903162 XM_047430821.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.292

Genes affected

LOC124903162 (HGNC:):

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=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.308 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124903162	XM_047430821.1	c.53+18063A>G		intron_variant
LINC00548	NR_033877.1	n.412-1638A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00598	ENST00000615947.1	n.219+18063A>G		intron_variant, non_coding_transcript_variant		4
LINC00598	ENST00000617777.1	n.412-1638A>G		intron_variant, non_coding_transcript_variant		2
LINC00598	ENST00000638084.1	n.839-306A>G		intron_variant, non_coding_transcript_variant		5
LINC00598	ENST00000654662.1	n.622-306A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.130 AC: 19697 AN: 151818 Hom.: 1503 Cov.: 31

Gnomad AFR AF: 0.101

Gnomad AMI AF: 0.111

Gnomad AMR AF: 0.210

Gnomad ASJ AF: 0.174

Gnomad EAS AF: 0.321

Gnomad SAS AF: 0.132

Gnomad FIN AF: 0.0856

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.118

Gnomad OTH AF: 0.150

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

GnomAD4 genome AF: 0.130 AC: 19704 AN: 151938 Hom.: 1500 Cov.: 31 AF XY: 0.129 AC XY: 9604 AN XY: 74256

Gnomad4 AFR AF: 0.101

Gnomad4 AMR AF: 0.210

Gnomad4 ASJ AF: 0.174

Gnomad4 EAS AF: 0.321

Gnomad4 SAS AF: 0.132

Gnomad4 FIN AF: 0.0856

Gnomad4 NFE AF: 0.118

Gnomad4 OTH AF: 0.149

Alfa AF: 0.120 Hom.: 157

Bravo AF: 0.142

Asia WGS AF: 0.185 AC: 645 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	7.5
Dann	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9566498; hg19: chr13-40773652; COSMIC: COSV69347832;