13-40233346-G-C

Position:

• chr13-40233346-G-C

Variant summary

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

The ENST00000615947.1(LINC00598):​n.47-15596C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.253 in 152,078 control chromosomes in the GnomAD database, including 5,225 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 0.25 (5225 hom., cov: 32)
• Consequence: LINC00598 ENST00000615947.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.299

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=-0.65).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.438 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC00598	ENST00000615947.1	n.47-15596C>G		intron_variant		4
LINC00598	ENST00000637438.1	n.401-26294C>G		intron_variant		5
LINC00598	ENST00000638084.1	n.406-15596C>G		intron_variant		5
LINC00598	ENST00000654662.1	n.553-32455C>G		intron_variant

Frequencies

GnomAD3 genomes AF: 0.253 AC: 38452 AN: 151960 Hom.: 5210 Cov.: 32

Gnomad AFR AF: 0.171

Gnomad AMI AF: 0.352

Gnomad AMR AF: 0.279

Gnomad ASJ AF: 0.310

Gnomad EAS AF: 0.453

Gnomad SAS AF: 0.278

Gnomad FIN AF: 0.337

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.261

Gnomad OTH AF: 0.299

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

GnomAD4 genome AF: 0.253 AC: 38488 AN: 152078 Hom.: 5225 Cov.: 32 AF XY: 0.259 AC XY: 19237 AN XY: 74342

Gnomad4 AFR AF: 0.171

Gnomad4 AMR AF: 0.279

Gnomad4 ASJ AF: 0.310

Gnomad4 EAS AF: 0.453

Gnomad4 SAS AF: 0.279

Gnomad4 FIN AF: 0.337

Gnomad4 NFE AF: 0.261

Gnomad4 OTH AF: 0.304

Alfa AF: 0.270 Hom.: 3175

Bravo AF: 0.246

Asia WGS AF: 0.378 AC: 1312 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	2.9
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10492681; hg19: chr13-40807483;