rs9566498

Variant names:

• chr13-40199515-T-C
• rs9566498
• XM_047430821.1:c.53+18063A>G

Your query was ambiguous. Multiple possible variants found:

• chr13-40199515-T-C
• chr13-40199515-T-G

Variant summary

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

The ENST00000617777.1(LINC00598):​n.412-1638A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.13 in 151,938 control chromosomes in the GnomAD database, including 1,500 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 0.13 (1500 hom., cov: 31)
• Consequence: LINC00598 ENST00000617777.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.292
• Publications: 1 publications found

Genes affected

LOC124903162 (HGNC:):

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

LINC00548 (HGNC:43683): (long intergenic non-protein coding RNA 548)

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 = 0.308 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000617777.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00548	NR_033877.1		n.412-1638A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00598	ENST00000615947.1	TSL:4	n.219+18063A>G		intron	N/A
	LINC00598	ENST00000617777.1	TSL:2	n.412-1638A>G		intron	N/A
	LINC00598	ENST00000638084.1	TSL:5	n.839-306A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.130 AC: 19697 AN: 151818 Hom.: 1503 Cov.: 31

Gnomad AFR AF: 0.101

Gnomad AMI AF: 0.111

Gnomad AMR AF: 0.210

Gnomad ASJ AF: 0.174

Gnomad EAS AF: 0.321

Gnomad SAS AF: 0.132

Gnomad FIN AF: 0.0856

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.118

Gnomad OTH AF: 0.150

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

GnomAD4 genome AF: 0.130 AC: 19704 AN: 151938 Hom.: 1500 Cov.: 31 AF XY: 0.129 AC XY: 9604 AN XY: 74256

African (AFR) AF: 0.101 AC: 4199 AN: 41436

American (AMR) AF: 0.210 AC: 3202 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.174 AC: 604 AN: 3472

East Asian (EAS) AF: 0.321 AC: 1647 AN: 5128

South Asian (SAS) AF: 0.132 AC: 633 AN: 4798

European-Finnish (FIN) AF: 0.0856 AC: 905 AN: 10570

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.118 AC: 8047 AN: 67968

Other (OTH) AF: 0.149 AC: 314 AN: 2108

Alfa AF: 0.119 Hom.: 163

Bravo AF: 0.142

Asia WGS AF: 0.185 AC: 645 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	7.5
DANN	Benign	0.60
PhyloP100		0.29

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs9566498;

hg19: chr13-40773652;

COSMIC: COSV69347832;