rs9315762

chr13-40167770-C-T

Variant summary

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

The XM_047430821.1(LOC124903162):c.54-48245G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.157 in 152,228 control chromosomes in the GnomAD database, including 2,445 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 0.16 (2445 hom., cov: 33)
• Consequence: LOC124903162 XM_047430821.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.593

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=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.27 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124903162	XM_047430821.1	c.54-48245G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00598	ENST00000615947.1	n.219+49808G>A		intron_variant, non_coding_transcript_variant		4
LINC00598	ENST00000635966.1	n.64-6073G>A		intron_variant, non_coding_transcript_variant		5
LINC00598	ENST00000653296.1	n.106+3332G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.157 AC: 23893 AN: 152110 Hom.: 2450 Cov.: 33

Gnomad AFR AF: 0.0378

Gnomad AMI AF: 0.125

Gnomad AMR AF: 0.277

Gnomad ASJ AF: 0.205

Gnomad EAS AF: 0.255

Gnomad SAS AF: 0.132

Gnomad FIN AF: 0.167

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.193

Gnomad OTH AF: 0.177

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

GnomAD4 genome AF: 0.157 AC: 23884 AN: 152228 Hom.: 2445 Cov.: 33 AF XY: 0.157 AC XY: 11678 AN XY: 74424

Gnomad4 AFR AF: 0.0377

Gnomad4 AMR AF: 0.277

Gnomad4 ASJ AF: 0.205

Gnomad4 EAS AF: 0.254

Gnomad4 SAS AF: 0.132

Gnomad4 FIN AF: 0.167

Gnomad4 NFE AF: 0.193

Gnomad4 OTH AF: 0.177

Alfa AF: 0.185 Hom.: 1548

Bravo AF: 0.162

Asia WGS AF: 0.150 AC: 523 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	1.6
Dann	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9315762; hg19: chr13-40741907;