13-40336251-C-A

Position:

• chr13-40336251-C-A

Variant summary

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

The ENST00000400432.4(LINC00598):​n.559+7706G>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 0.521 in 152,036 control chromosomes in the GnomAD database, including 21,365 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 0.52 (21365 hom., cov: 32)
• Consequence: LINC00598 ENST00000400432.4 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0820

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=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.804 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	ENST00000400432.4	n.559+7706G>T		intron_variant, non_coding_transcript_variant		5
LINC00598	ENST00000636192.2	n.620+7706G>T		intron_variant, non_coding_transcript_variant		5
LINC00598	ENST00000637438.1	n.205+13858G>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.521 AC: 79153 AN: 151920 Hom.: 21336 Cov.: 32

Gnomad AFR AF: 0.385

Gnomad AMI AF: 0.523

Gnomad AMR AF: 0.653

Gnomad ASJ AF: 0.510

Gnomad EAS AF: 0.825

Gnomad SAS AF: 0.581

Gnomad FIN AF: 0.595

Gnomad MID AF: 0.434

Gnomad NFE AF: 0.536

Gnomad OTH AF: 0.529

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

GnomAD4 genome AF: 0.521 AC: 79214 AN: 152036 Hom.: 21365 Cov.: 32 AF XY: 0.530 AC XY: 39354 AN XY: 74320

Gnomad4 AFR AF: 0.384

Gnomad4 AMR AF: 0.654

Gnomad4 ASJ AF: 0.510

Gnomad4 EAS AF: 0.825

Gnomad4 SAS AF: 0.580

Gnomad4 FIN AF: 0.595

Gnomad4 NFE AF: 0.536

Gnomad4 OTH AF: 0.534

Alfa AF: 0.479 Hom.: 3658

Bravo AF: 0.523

Asia WGS AF: 0.697 AC: 2424 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.2
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4943770; hg19: chr13-40910388;