chr13-40366522-C-A

Position:

• chr13-40366522-C-A

Variant summary

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

The NR_024506.1(LINC00598):​n.664-16220G>T 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 0.102 in 152,204 control chromosomes in the GnomAD database, including 952 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 0.10 (952 hom., cov: 32)
• Consequence: LINC00598 NR_024506.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.50

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=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.228 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC00598	NR_024506.1	n.664-16220G>T		intron_variant, non_coding_transcript_variant
LINC00598	NR_024507.2	n.804-16220G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC00598	ENST00000636621.1	n.71-16220G>T		intron_variant, non_coding_transcript_variant		1
LINC00598	ENST00000400432.4	n.117-16220G>T		intron_variant, non_coding_transcript_variant		5
LINC00598	ENST00000636192.2	n.178-16220G>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.102 AC: 15506 AN: 152086 Hom.: 944 Cov.: 32

Gnomad AFR AF: 0.133

Gnomad AMI AF: 0.0932

Gnomad AMR AF: 0.157

Gnomad ASJ AF: 0.0303

Gnomad EAS AF: 0.239

Gnomad SAS AF: 0.0706

Gnomad FIN AF: 0.0781

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0705

Gnomad OTH AF: 0.0968

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

GnomAD4 genome AF: 0.102 AC: 15544 AN: 152204 Hom.: 952 Cov.: 32 AF XY: 0.104 AC XY: 7771 AN XY: 74420

Gnomad4 AFR AF: 0.133

Gnomad4 AMR AF: 0.158

Gnomad4 ASJ AF: 0.0303

Gnomad4 EAS AF: 0.239

Gnomad4 SAS AF: 0.0710

Gnomad4 FIN AF: 0.0781

Gnomad4 NFE AF: 0.0705

Gnomad4 OTH AF: 0.0958

Alfa AF: 0.0747 Hom.: 622

Bravo AF: 0.115

Asia WGS AF: 0.136 AC: 473 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	8.8
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1041211; hg19: chr13-40940659;