rs10492680

Variant names:

• chr13-40230699-A-G
• rs10492680
• ENST00000615947.1:n.47-12949T>C

Variant summary

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

The ENST00000615947.1(LINC00598):​n.47-12949T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.301 in 151,994 control chromosomes in the GnomAD database, including 7,656 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 0.30 (7656 hom., cov: 31)
• Consequence: LINC00598 ENST00000615947.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.95
• Publications: 4 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=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.449 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.47-12949T>C		intron_variant	Intron 1 of 3	4
LINC00598	ENST00000637438.1	n.401-23647T>C		intron_variant	Intron 2 of 3	5
LINC00598	ENST00000638084.1	n.406-12949T>C		intron_variant	Intron 2 of 5	5

Frequencies

GnomAD3 genomes AF: 0.301 AC: 45762 AN: 151876 Hom.: 7660 Cov.: 31

Gnomad AFR AF: 0.170

Gnomad AMI AF: 0.302

Gnomad AMR AF: 0.298

Gnomad ASJ AF: 0.273

Gnomad EAS AF: 0.104

Gnomad SAS AF: 0.466

Gnomad FIN AF: 0.372

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.376

Gnomad OTH AF: 0.277

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

GnomAD4 genome AF: 0.301 AC: 45764 AN: 151994 Hom.: 7656 Cov.: 31 AF XY: 0.302 AC XY: 22411 AN XY: 74312

African (AFR) AF: 0.170 AC: 7042 AN: 41434

American (AMR) AF: 0.298 AC: 4559 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.273 AC: 949 AN: 3470

East Asian (EAS) AF: 0.104 AC: 538 AN: 5178

South Asian (SAS) AF: 0.465 AC: 2232 AN: 4800

European-Finnish (FIN) AF: 0.372 AC: 3930 AN: 10574

Middle Eastern (MID) AF: 0.286 AC: 84 AN: 294

European-Non Finnish (NFE) AF: 0.376 AC: 25580 AN: 67942

Other (OTH) AF: 0.273 AC: 576 AN: 2112

Alfa AF: 0.347 Hom.: 16419

Bravo AF: 0.284

Asia WGS AF: 0.253 AC: 882 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.10
DANN	Benign	0.57
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs10492680; hg19: chr13-40804836;