5-601532-G-T

Variant names:

• chr5-601532-G-T
• rs3828570
• ENST00000782781.1:n.359+9915C>A

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000782781.1(CEP72-DT):​n.359+9915C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
• Consequence: CEP72-DT ENST00000782781.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.80
• Publications: 8 publications found

Genes affected

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

LOC105374608 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105374608	XR_007058672.1	n.572+22G>T		intron_variant	Intron 2 of 7
LOC105374608	XR_007058673.1	n.244+22G>T		intron_variant	Intron 1 of 5
LOC105374608	XR_007058674.1	n.244+22G>T		intron_variant	Intron 1 of 6
LOC105374608	XR_007058675.1	n.244+22G>T		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CEP72-DT	ENST00000782781.1	n.359+9915C>A		intron_variant	Intron 2 of 3
CEP72-DT	ENST00000782782.1	n.265+9915C>A		intron_variant	Intron 2 of 3
CEP72-DT	ENST00000782783.1	n.254-3044C>A		intron_variant	Intron 2 of 4
CEP72-DT	ENST00000782785.1	n.*27C>A		downstream_gene_variant

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 6628

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.0060
DANN	Benign	0.64
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs3828570; hg19: chr5-601647;