rs636555

chr10-104180236-C-T

Variant summary

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

The NM_025145.7(CFAP43):c.2290-304G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0976 in 152,182 control chromosomes in the GnomAD database, including 1,155 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 0.098 (1155 hom., cov: 32)
• Consequence: CFAP43 NM_025145.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.204

Genes affected

CFAP43 (HGNC:26684): (cilia and flagella associated protein 43) This gene encodes a member of the cilia- and flagella-associated protein family. [provided by RefSeq, Sep 2016]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.204 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CFAP43	NM_025145.7	c.2290-304G>A		intron_variant		ENST00000357060.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CFAP43	ENST00000357060.8	c.2290-304G>A		intron_variant		1	NM_025145.7	P1
CFAP43	ENST00000278064.7	c.2293-304G>A		intron_variant		1
CFAP43	ENST00000434629.5	c.372-304G>A		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.0974 AC: 14804 AN: 152064 Hom.: 1147 Cov.: 32

Gnomad AFR AF: 0.207

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.0595

Gnomad ASJ AF: 0.104

Gnomad EAS AF: 0.101

Gnomad SAS AF: 0.133

Gnomad FIN AF: 0.0150

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0509

Gnomad OTH AF: 0.0760

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

GnomAD4 genome AF: 0.0976 AC: 14850 AN: 152182 Hom.: 1155 Cov.: 32 AF XY: 0.0955 AC XY: 7105 AN XY: 74418

Gnomad4 AFR AF: 0.207

Gnomad4 AMR AF: 0.0595

Gnomad4 ASJ AF: 0.104

Gnomad4 EAS AF: 0.101

Gnomad4 SAS AF: 0.133

Gnomad4 FIN AF: 0.0150

Gnomad4 NFE AF: 0.0510

Gnomad4 OTH AF: 0.0828

Alfa AF: 0.0683 Hom.: 117

Bravo AF: 0.104

Asia WGS AF: 0.157 AC: 545 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	1.3
Dann	Benign	0.45

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: rs636555; hg19: chr10-105939994;