rs11739663

Variant names:

• chr5-593968-T-C
• rs11739663
• ENST00000782781.1:n.359+17479A>G

Variant summary

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

The ENST00000782781.1(CEP72-DT):​n.359+17479A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.279 in 152,076 control chromosomes in the GnomAD database, including 7,092 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 0.28 (7092 hom., cov: 33)
• Consequence: CEP72-DT ENST00000782781.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0450
• Publications: 56 publications found

Genes affected

CEP72-DT (HGNC:55563): (CEP72 divergent transcript)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.464 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
CEP72-DT	ENST00000782781.1	n.359+17479A>G		intron_variant	Intron 2 of 3
CEP72-DT	ENST00000782782.1	n.265+17479A>G		intron_variant	Intron 2 of 3
CEP72-DT	ENST00000782783.1	n.382+4392A>G		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.279 AC: 42355 AN: 151958 Hom.: 7076 Cov.: 33

Gnomad AFR AF: 0.469

Gnomad AMI AF: 0.251

Gnomad AMR AF: 0.223

Gnomad ASJ AF: 0.218

Gnomad EAS AF: 0.00888

Gnomad SAS AF: 0.209

Gnomad FIN AF: 0.151

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.225

Gnomad OTH AF: 0.254

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

GnomAD4 genome AF: 0.279 AC: 42405 AN: 152076 Hom.: 7092 Cov.: 33 AF XY: 0.271 AC XY: 20160 AN XY: 74322

African (AFR) AF: 0.469 AC: 19454 AN: 41440

American (AMR) AF: 0.222 AC: 3401 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.218 AC: 757 AN: 3470

East Asian (EAS) AF: 0.00890 AC: 46 AN: 5170

South Asian (SAS) AF: 0.209 AC: 1006 AN: 4818

European-Finnish (FIN) AF: 0.151 AC: 1600 AN: 10594

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.225 AC: 15310 AN: 67974

Other (OTH) AF: 0.252 AC: 533 AN: 2114

Alfa AF: 0.238 Hom.: 19465

Bravo AF: 0.292

Asia WGS AF: 0.127 AC: 443 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	12
DANN	Benign	0.65
PhyloP100		-0.045

Splicing

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

Other links and lift over

dbSNP: rs11739663; hg19: chr5-594083;