chr13-40336251-C-A

Variant names:

• chr13-40336251-C-A
• rs4943770
• ENST00000400432.4:n.559+7706G>T

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 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
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00598	ENST00000400432.4	n.559+7706G>T		intron_variant	Intron 3 of 3	5
LINC00598	ENST00000636192.2	n.620+7706G>T		intron_variant	Intron 3 of 3	5
LINC00598	ENST00000637438.1	n.205+13858G>T		intron_variant	Intron 1 of 3	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;