13-40374014-C-T

Position:

• chr13-40374014-C-T

Variant summary

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

The NR_024506.1(LINC00598):​n.664-23712G>A 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 0.965 in 152,322 control chromosomes in the GnomAD database, including 70,875 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 0.96 (70875 hom., cov: 32)
• Consequence: LINC00598 NR_024506.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.68

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=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.972 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC00598	NR_024506.1	n.664-23712G>A		intron_variant, non_coding_transcript_variant
LINC00598	NR_024507.2	n.804-23712G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00598	ENST00000636621.1	n.71-23712G>A		intron_variant, non_coding_transcript_variant		1
LINC00598	ENST00000400432.4	n.117-23712G>A		intron_variant, non_coding_transcript_variant		5
LINC00598	ENST00000636192.2	n.178-23712G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.965 AC: 146807 AN: 152204 Hom.: 70821 Cov.: 32

Gnomad AFR AF: 0.945

Gnomad AMI AF: 0.953

Gnomad AMR AF: 0.976

Gnomad ASJ AF: 0.970

Gnomad EAS AF: 0.988

Gnomad SAS AF: 0.937

Gnomad FIN AF: 0.938

Gnomad MID AF: 0.930

Gnomad NFE AF: 0.979

Gnomad OTH AF: 0.961

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

GnomAD4 genome AF: 0.965 AC: 146920 AN: 152322 Hom.: 70875 Cov.: 32 AF XY: 0.963 AC XY: 71702 AN XY: 74474

Gnomad4 AFR AF: 0.945

Gnomad4 AMR AF: 0.976

Gnomad4 ASJ AF: 0.970

Gnomad4 EAS AF: 0.988

Gnomad4 SAS AF: 0.936

Gnomad4 FIN AF: 0.938

Gnomad4 NFE AF: 0.979

Gnomad4 OTH AF: 0.961

Alfa AF: 0.969 Hom.: 10017

Bravo AF: 0.967

Asia WGS AF: 0.956 AC: 3327 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.016
DANN	Benign	0.17

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs913246; hg19: chr13-40948151;