chr10-104393141-C-A

Variant names:

• chr10-104393141-C-A
• rs10509770
• NM_001008723.2:c.1528-188C>A

Variant summary

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

The NM_001008723.2(CFAP58):​c.1528-188C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0481 in 152,042 control chromosomes in the GnomAD database, including 395 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 0.048 (395 hom., cov: 32)
• Consequence: CFAP58 NM_001008723.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.120
• Publications: 0 publications found

Genes affected

CFAP58 (HGNC:26676): (cilia and flagella associated protein 58) Involved in protein localization to motile cilium; sperm axoneme assembly; and sperm mitochondrial sheath assembly. Located in sperm midpiece. Implicated in spermatogenic failure 49. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.131 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CFAP58	NM_001008723.2	c.1528-188C>A		intron_variant	Intron 10 of 17	ENST00000369704.8	NP_001008723.1
CFAP58	NM_001400226.1	c.1474-188C>A		intron_variant	Intron 11 of 18		NP_001387155.1
CFAP58	NM_001400227.1	c.1474-188C>A		intron_variant	Intron 10 of 17		NP_001387156.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CFAP58	ENST00000369704.8	c.1528-188C>A		intron_variant	Intron 10 of 17	1	NM_001008723.2	ENSP00000358718.3

Frequencies

GnomAD3 genomes AF: 0.0479 AC: 7283 AN: 151924 Hom.: 392 Cov.: 32

Gnomad AFR AF: 0.133

Gnomad AMI AF: 0.0450

Gnomad AMR AF: 0.0210

Gnomad ASJ AF: 0.0144

Gnomad EAS AF: 0.0168

Gnomad SAS AF: 0.0601

Gnomad FIN AF: 0.00824

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0121

Gnomad OTH AF: 0.0350

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

GnomAD4 genome AF: 0.0481 AC: 7312 AN: 152042 Hom.: 395 Cov.: 32 AF XY: 0.0466 AC XY: 3464 AN XY: 74324

African (AFR) AF: 0.134 AC: 5530 AN: 41420

American (AMR) AF: 0.0210 AC: 321 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0144 AC: 50 AN: 3468

East Asian (EAS) AF: 0.0168 AC: 87 AN: 5172

South Asian (SAS) AF: 0.0597 AC: 288 AN: 4824

European-Finnish (FIN) AF: 0.00824 AC: 87 AN: 10556

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.0121 AC: 825 AN: 68000

Other (OTH) AF: 0.0351 AC: 74 AN: 2108

Alfa AF: 0.0205 Hom.: 30

Bravo AF: 0.0516

Asia WGS AF: 0.0470 AC: 162 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.0
DANN	Benign	0.57
PhyloP100		0.12
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs10509770; hg19: chr10-106152899;