rs163771

Positions:

• chr1-229333603-G-A

Variant summary

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

The NM_145257.5(CCSAP):​c.368-6597C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.393 in 151,868 control chromosomes in the GnomAD database, including 12,038 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 0.39 (12038 hom., cov: 31)
• Consequence: CCSAP NM_145257.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.358

Genes affected

CCSAP (HGNC:29578): (centriole, cilia and spindle associated protein) Enables microtubule binding activity. Involved in mitotic spindle microtubule depolymerization and regulation of mitotic spindle assembly. Located in axon; ciliary transition zone; and cytoskeleton. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.47 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CCSAP	NM_145257.5	c.368-6597C>T		intron_variant		ENST00000284617.7
CCSAP	NM_001410936.1	c.26-6597C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCSAP	ENST00000284617.7	c.368-6597C>T		intron_variant		1	NM_145257.5	P1
CCSAP	ENST00000366687.5	c.368-6597C>T		intron_variant		1		P1
CCSAP	ENST00000483092.1	n.799-6045C>T		intron_variant, non_coding_transcript_variant		1
CCSAP	ENST00000366686.1	c.26-6597C>T		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.393 AC: 59607 AN: 151754 Hom.: 12010 Cov.: 31

Gnomad AFR AF: 0.474

Gnomad AMI AF: 0.490

Gnomad AMR AF: 0.334

Gnomad ASJ AF: 0.518

Gnomad EAS AF: 0.242

Gnomad SAS AF: 0.231

Gnomad FIN AF: 0.353

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.378

Gnomad OTH AF: 0.374

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

GnomAD4 genome AF: 0.393 AC: 59681 AN: 151868 Hom.: 12038 Cov.: 31 AF XY: 0.384 AC XY: 28499 AN XY: 74206

Gnomad4 AFR AF: 0.475

Gnomad4 AMR AF: 0.334

Gnomad4 ASJ AF: 0.518

Gnomad4 EAS AF: 0.243

Gnomad4 SAS AF: 0.232

Gnomad4 FIN AF: 0.353

Gnomad4 NFE AF: 0.378

Gnomad4 OTH AF: 0.370

Alfa AF: 0.382 Hom.: 2239

Bravo AF: 0.396

Asia WGS AF: 0.247 AC: 860 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.79
DANN	Benign	0.64

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs163771; hg19: chr1-229469350;