13-40233346-G-C

Variant names:

• chr13-40233346-G-C
• rs10492681
• ENST00000615947.1:n.47-15596C>G

Variant summary

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

The ENST00000615947.1(LINC00598):​n.47-15596C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.253 in 152,078 control chromosomes in the GnomAD database, including 5,225 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 0.25 (5225 hom., cov: 32)
• Consequence: LINC00598 ENST00000615947.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.299
• Publications: 12 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.65).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.438 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	ENST00000615947.1	n.47-15596C>G		intron_variant	Intron 1 of 3	4
LINC00598	ENST00000637438.1	n.401-26294C>G		intron_variant	Intron 2 of 3	5
LINC00598	ENST00000638084.1	n.406-15596C>G		intron_variant	Intron 2 of 5	5

Frequencies

GnomAD3 genomes AF: 0.253 AC: 38452 AN: 151960 Hom.: 5210 Cov.: 32

Gnomad AFR AF: 0.171

Gnomad AMI AF: 0.352

Gnomad AMR AF: 0.279

Gnomad ASJ AF: 0.310

Gnomad EAS AF: 0.453

Gnomad SAS AF: 0.278

Gnomad FIN AF: 0.337

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.261

Gnomad OTH AF: 0.299

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

GnomAD4 genome AF: 0.253 AC: 38488 AN: 152078 Hom.: 5225 Cov.: 32 AF XY: 0.259 AC XY: 19237 AN XY: 74342

African (AFR) AF: 0.171 AC: 7103 AN: 41486

American (AMR) AF: 0.279 AC: 4260 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.310 AC: 1075 AN: 3468

East Asian (EAS) AF: 0.453 AC: 2346 AN: 5178

South Asian (SAS) AF: 0.279 AC: 1343 AN: 4820

European-Finnish (FIN) AF: 0.337 AC: 3558 AN: 10558

Middle Eastern (MID) AF: 0.259 AC: 76 AN: 294

European-Non Finnish (NFE) AF: 0.261 AC: 17764 AN: 67968

Other (OTH) AF: 0.304 AC: 643 AN: 2112

Alfa AF: 0.270 Hom.: 3175

Bravo AF: 0.246

Asia WGS AF: 0.378 AC: 1312 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	2.9
DANN	Benign	0.67
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs10492681; hg19: chr13-40807483;