rs6632450

Variant names:

• chrX-35975337-C-T
• rs6632450
• NM_001304548.2:c.2445C>T

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_Strong BP7 BA1

The NM_001304548.2(CFAP47):​c.2445C>T​(p.Asp815Asp) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0921 in 1,189,464 control chromosomes in the GnomAD database, including 5,531 homozygotes. There are 36,583 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 0.15 (1222 hom., 4929 hem., cov: 23)
  • Exomes 𝑓: 0.086 (4309 hom. 31654 hem.)
• Consequence: CFAP47 NM_001304548.2 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0160

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]

ACMG classification

Verdict is Benign. Variant got -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BP7: Synonymous conserved (PhyloP=0.016 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.281 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CFAP47	NM_001304548.2	c.2445C>T	p.Asp815Asp	synonymous_variant	Exon 14 of 64	ENST00000378653.8	NP_001291477.1
CFAP47	NM_152632.4	c.2445C>T	p.Asp815Asp	synonymous_variant	Exon 14 of 16		NP_689845.2
CFAP47	XM_017029452.2	c.2445C>T	p.Asp815Asp	synonymous_variant	Exon 14 of 54		XP_016884941.1
CFAP47	XM_017029453.2	c.2445C>T	p.Asp815Asp	synonymous_variant	Exon 14 of 36		XP_016884942.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CFAP47	ENST00000378653.8	c.2445C>T	p.Asp815Asp	synonymous_variant	Exon 14 of 64	5	NM_001304548.2	ENSP00000367922.5
CFAP47	ENST00000493930.1	n.*82C>T		non_coding_transcript_exon_variant	Exon 14 of 16	1		ENSP00000433564.1
CFAP47	ENST00000493930.1	n.*82C>T		3_prime_UTR_variant	Exon 14 of 16	1		ENSP00000433564.1
CFAP47	ENST00000297866.9	c.2445C>T	p.Asp815Asp	synonymous_variant	Exon 14 of 16	2		ENSP00000297866.5

Frequencies

GnomAD3 genomes AF: 0.149 AC: 16452 AN: 110696 Hom.: 1215 Cov.: 23 AF XY: 0.149 AC XY: 4907 AN XY: 32956

Gnomad AFR AF: 0.253

Gnomad AMI AF: 0.0438

Gnomad AMR AF: 0.231

Gnomad ASJ AF: 0.100

Gnomad EAS AF: 0.296

Gnomad SAS AF: 0.259

Gnomad FIN AF: 0.123

Gnomad MID AF: 0.115

Gnomad NFE AF: 0.0637

Gnomad OTH AF: 0.162

GnomAD3 exomes AF: 0.149 AC: 25989 AN: 173981 Hom.: 1914 AF XY: 0.140 AC XY: 8340 AN XY: 59771

Gnomad AFR exome AF: 0.266

Gnomad AMR exome AF: 0.243

Gnomad ASJ exome AF: 0.110

Gnomad EAS exome AF: 0.307

Gnomad SAS exome AF: 0.252

Gnomad FIN exome AF: 0.112

Gnomad NFE exome AF: 0.0637

Gnomad OTH exome AF: 0.132

GnomAD4 exome AF: 0.0863 AC: 93087 AN: 1078717 Hom.: 4309 Cov.: 27 AF XY: 0.0913 AC XY: 31654 AN XY: 346631

Gnomad4 AFR exome AF: 0.265

Gnomad4 AMR exome AF: 0.250

Gnomad4 ASJ exome AF: 0.106

Gnomad4 EAS exome AF: 0.254

Gnomad4 SAS exome AF: 0.241

Gnomad4 FIN exome AF: 0.112

Gnomad4 NFE exome AF: 0.0552

Gnomad4 OTH exome AF: 0.109

GnomAD4 genome AF: 0.149 AC: 16500 AN: 110747 Hom.: 1222 Cov.: 23 AF XY: 0.149 AC XY: 4929 AN XY: 33017

Gnomad4 AFR AF: 0.254

Gnomad4 AMR AF: 0.232

Gnomad4 ASJ AF: 0.100

Gnomad4 EAS AF: 0.296

Gnomad4 SAS AF: 0.258

Gnomad4 FIN AF: 0.123

Gnomad4 NFE AF: 0.0637

Gnomad4 OTH AF: 0.171

Alfa AF: 0.115 Hom.: 1461

Bravo AF: 0.162

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.14
DANN	Benign	0.19

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.090		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: rs6632450; hg19: chrX-35993454; COSMIC: COSV52882191;