13-99928947-C-T

Variant names:

• chr13-99928947-C-T
• rs9517921
• ENST00000656974.1:n.191+26698G>A

Variant summary

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

The ENST00000656974.1(ENSG00000286757):​n.191+26698G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.18 in 151,984 control chromosomes in the GnomAD database, including 2,596 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 (2596 hom., cov: 30)
• Consequence: ENSG00000286757 ENST00000656974.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.305
• Publications: 3 publications found

Genes affected

ENSG00000286757 (HGNC:):

CLYBL-AS3 (HGNC:56191): (CLYBL antisense RNA 3)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.241 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CLYBL-AS3	NR_120421.1	n.83+28136G>A		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286757	ENST00000656974.1	n.191+26698G>A		intron_variant	Intron 1 of 2
ENSG00000286757	ENST00000659729.1	n.99+26698G>A		intron_variant	Intron 1 of 1
ENSG00000286757	ENST00000661077.2	n.105+26698G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.180 AC: 27362 AN: 151868 Hom.: 2591 Cov.: 30

Gnomad AFR AF: 0.196

Gnomad AMI AF: 0.254

Gnomad AMR AF: 0.247

Gnomad ASJ AF: 0.172

Gnomad EAS AF: 0.0595

Gnomad SAS AF: 0.175

Gnomad FIN AF: 0.112

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.176

Gnomad OTH AF: 0.169

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

GnomAD4 genome AF: 0.180 AC: 27400 AN: 151984 Hom.: 2596 Cov.: 30 AF XY: 0.178 AC XY: 13243 AN XY: 74294

African (AFR) AF: 0.196 AC: 8136 AN: 41448

American (AMR) AF: 0.248 AC: 3780 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.172 AC: 595 AN: 3462

East Asian (EAS) AF: 0.0595 AC: 306 AN: 5146

South Asian (SAS) AF: 0.174 AC: 838 AN: 4818

European-Finnish (FIN) AF: 0.112 AC: 1180 AN: 10580

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.176 AC: 11937 AN: 67970

Other (OTH) AF: 0.167 AC: 353 AN: 2110

Alfa AF: 0.183 Hom.: 4385

Bravo AF: 0.195

Asia WGS AF: 0.120 AC: 416 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.8
DANN	Benign	0.30
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs9517921; hg19: chr13-100581201;