rs6629078

Variant names:

• chrX-36366537-A-C
• rs6629078
• NM_001304548.2:c.9024-429A>C

Variant summary

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

The NM_001304548.2(CFAP47):​c.9024-429A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0937 in 111,372 control chromosomes in the GnomAD database, including 379 homozygotes. There are 3,228 hemizygotes in GnomAD. 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 0.094 (379 hom., 3228 hem., cov: 23)
• Consequence: CFAP47 NM_001304548.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.727
• Publications: 1 publications found

Genes affected

CFAP47 (HGNC:26708): (cilia and flagella associated protein 47) While this gene is well-supported by transcript data, no functional information on its protein product is currently available. [provided by RefSeq, Dec 2009]

CFAP47 Gene-Disease associations (from GenCC):

• polycystic kidney disease

  Inheritance: XL Classification: LIMITED Submitted by: University of Washington Center for Rare Disease Research (UW-CRDR)
• spermatogenic failure, X-linked, 3

  Inheritance: XL Classification: LIMITED Submitted by: ClinGen, Ambry Genetics

ENSG00000226484 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.216 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CFAP47	NM_001304548.2	c.9024-429A>C		intron_variant	Intron 61 of 63	ENST00000378653.8	NP_001291477.1
LOC101928627	NR_110412.1	n.1685-735T>G		intron_variant	Intron 7 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CFAP47	ENST00000378653.8	c.9024-429A>C		intron_variant	Intron 61 of 63	5	NM_001304548.2	ENSP00000367922.5
CFAP47	ENST00000630521.1	c.170+5036A>C		intron_variant	Intron 1 of 1	3		ENSP00000485710.1
CFAP47	ENST00000446478.1	n.177-429A>C		intron_variant	Intron 1 of 2	3
ENSG00000226484	ENST00000455438.2	n.1685-735T>G		intron_variant	Intron 7 of 7	2

Frequencies

GnomAD3 genomes AF: 0.0935 AC: 10411 AN: 111322 Hom.: 374 Cov.: 23

Gnomad AFR AF: 0.0832

Gnomad AMI AF: 0.0739

Gnomad AMR AF: 0.111

Gnomad ASJ AF: 0.0777

Gnomad EAS AF: 0.229

Gnomad SAS AF: 0.212

Gnomad FIN AF: 0.128

Gnomad MID AF: 0.0714

Gnomad NFE AF: 0.0782

Gnomad OTH AF: 0.0904

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

GnomAD4 genome AF: 0.0937 AC: 10433 AN: 111372 Hom.: 379 Cov.: 23 AF XY: 0.0958 AC XY: 3228 AN XY: 33682

African (AFR) AF: 0.0833 AC: 2566 AN: 30810

American (AMR) AF: 0.111 AC: 1162 AN: 10426

Ashkenazi Jewish (ASJ) AF: 0.0777 AC: 205 AN: 2637

East Asian (EAS) AF: 0.229 AC: 804 AN: 3510

South Asian (SAS) AF: 0.211 AC: 567 AN: 2683

European-Finnish (FIN) AF: 0.128 AC: 771 AN: 6010

Middle Eastern (MID) AF: 0.0787 AC: 17 AN: 216

European-Non Finnish (NFE) AF: 0.0782 AC: 4137 AN: 52880

Other (OTH) AF: 0.101 AC: 154 AN: 1523

Alfa AF: 0.0972 Hom.: 623

Bravo AF: 0.0927

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.12
DANN	Benign	0.61
PhyloP100		-0.73
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs6629078; hg19: chrX-36384652;