rs9315762

Variant names:

• chr13-40167770-C-T
• rs9315762
• ENST00000615947.1:n.219+49808G>A

Variant summary

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

The ENST00000615947.1(LINC00598):​n.219+49808G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.157 in 152,228 control chromosomes in the GnomAD database, including 2,445 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 0.16 (2445 hom., cov: 33)
• Consequence: LINC00598 ENST00000615947.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.593
• Publications: 7 publications found

Genes affected

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

LOC124903162 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.27 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124903162	XM_047430821.1	c.54-48245G>A		intron_variant	Intron 1 of 4		XP_047286777.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00598	ENST00000615947.1	n.219+49808G>A		intron_variant	Intron 2 of 3	4
LINC00598	ENST00000635966.1	n.64-6073G>A		intron_variant	Intron 1 of 7	5
LINC00598	ENST00000653296.1	n.106+3332G>A		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.157 AC: 23893 AN: 152110 Hom.: 2450 Cov.: 33

Gnomad AFR AF: 0.0378

Gnomad AMI AF: 0.125

Gnomad AMR AF: 0.277

Gnomad ASJ AF: 0.205

Gnomad EAS AF: 0.255

Gnomad SAS AF: 0.132

Gnomad FIN AF: 0.167

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.193

Gnomad OTH AF: 0.177

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

GnomAD4 genome AF: 0.157 AC: 23884 AN: 152228 Hom.: 2445 Cov.: 33 AF XY: 0.157 AC XY: 11678 AN XY: 74424

African (AFR) AF: 0.0377 AC: 1567 AN: 41560

American (AMR) AF: 0.277 AC: 4236 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.205 AC: 711 AN: 3470

East Asian (EAS) AF: 0.254 AC: 1314 AN: 5176

South Asian (SAS) AF: 0.132 AC: 639 AN: 4824

European-Finnish (FIN) AF: 0.167 AC: 1770 AN: 10574

Middle Eastern (MID) AF: 0.187 AC: 55 AN: 294

European-Non Finnish (NFE) AF: 0.193 AC: 13105 AN: 68008

Other (OTH) AF: 0.177 AC: 373 AN: 2108

Alfa AF: 0.169 Hom.: 2257

Bravo AF: 0.162

Asia WGS AF: 0.150 AC: 523 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.6
DANN	Benign	0.61
PhyloP100		-0.59

Splicing

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

Other links and lift over

dbSNP: rs9315762; hg19: chr13-40741907;