rs924607

chr5-609978-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_103444.1(CEP72-DT):n.366+1469G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.325 in 151,972 control chromosomes in the GnomAD database, including 9,422 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 0.33 (9422 hom., cov: 32)
• Consequence: CEP72-DT NR_103444.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.679

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.411 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CEP72-DT	NR_103444.1	n.366+1469G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CEP72-DT	ENST00000506629.1	n.366+1469G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.325 AC: 49415 AN: 151854 Hom.: 9417 Cov.: 32

Gnomad AFR AF: 0.115

Gnomad AMI AF: 0.383

Gnomad AMR AF: 0.327

Gnomad ASJ AF: 0.364

Gnomad EAS AF: 0.340

Gnomad SAS AF: 0.385

Gnomad FIN AF: 0.518

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.415

Gnomad OTH AF: 0.344

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

GnomAD4 genome AF: 0.325 AC: 49431 AN: 151972 Hom.: 9422 Cov.: 32 AF XY: 0.332 AC XY: 24671 AN XY: 74296

Gnomad4 AFR AF: 0.115

Gnomad4 AMR AF: 0.327

Gnomad4 ASJ AF: 0.364

Gnomad4 EAS AF: 0.340

Gnomad4 SAS AF: 0.387

Gnomad4 FIN AF: 0.518

Gnomad4 NFE AF: 0.415

Gnomad4 OTH AF: 0.345

Alfa AF: 0.341 Hom.: 1864

Bravo AF: 0.299

Asia WGS AF: 0.327 AC: 1139 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	4.2
Dann	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs924607; hg19: chr5-610093;