13-40535292-A-C

Variant names:

• chr13-40535292-A-C
• rs2755237
• ENST00000615137.1:n.142+374T>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000615137.1(LINC00598):​n.142+374T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.176 in 152,216 control chromosomes in the GnomAD database, including 2,580 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 0.18 (2580 hom., cov: 33)
• Consequence: LINC00598 ENST00000615137.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.118
• Publications: 28 publications found

Genes affected

LINC00598 (HGNC:42770): (long intergenic non-protein coding RNA 598)

ENSG00000288542 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.307 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000615137.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00598	ENST00000615137.1	TSL:3	n.142+374T>G		intron	N/A
	ENSG00000288542	ENST00000636651.2	TSL:5	n.1459+24217T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.176 AC: 26753 AN: 152098 Hom.: 2577 Cov.: 33

Gnomad AFR AF: 0.223

Gnomad AMI AF: 0.255

Gnomad AMR AF: 0.171

Gnomad ASJ AF: 0.157

Gnomad EAS AF: 0.320

Gnomad SAS AF: 0.114

Gnomad FIN AF: 0.102

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.151

Gnomad OTH AF: 0.222

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

GnomAD4 genome AF: 0.176 AC: 26777 AN: 152216 Hom.: 2580 Cov.: 33 AF XY: 0.172 AC XY: 12778 AN XY: 74430

African (AFR) AF: 0.224 AC: 9282 AN: 41520

American (AMR) AF: 0.171 AC: 2611 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.157 AC: 546 AN: 3472

East Asian (EAS) AF: 0.320 AC: 1656 AN: 5170

South Asian (SAS) AF: 0.113 AC: 547 AN: 4820

European-Finnish (FIN) AF: 0.102 AC: 1077 AN: 10608

Middle Eastern (MID) AF: 0.282 AC: 83 AN: 294

European-Non Finnish (NFE) AF: 0.151 AC: 10273 AN: 68016

Other (OTH) AF: 0.223 AC: 470 AN: 2110

Alfa AF: 0.166 Hom.: 9614

Bravo AF: 0.185

Asia WGS AF: 0.213 AC: 741 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	17
DANN	Benign	0.64
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs2755237; hg19: chr13-41109429;