rs11594962

chr10-104156867-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.3541-4141G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0418 in 152,138 control chromosomes in the GnomAD database, including 193 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 0.042 (193 hom., cov: 32)
• Consequence: CFAP43 NM_025145.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.281

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=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0647 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CFAP43	NM_025145.7	c.3541-4141G>A		intron_variant		ENST00000357060.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CFAP43	ENST00000357060.8	c.3541-4141G>A		intron_variant		1	NM_025145.7	P1
CFAP43	ENST00000434629.5	c.1623-4141G>A		intron_variant		1
CFAP43	ENST00000457071.5	c.87-4141G>A		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.0419 AC: 6366 AN: 152020 Hom.: 193 Cov.: 32

Gnomad AFR AF: 0.0109

Gnomad AMI AF: 0.0789

Gnomad AMR AF: 0.0349

Gnomad ASJ AF: 0.0130

Gnomad EAS AF: 0.00135

Gnomad SAS AF: 0.00518

Gnomad FIN AF: 0.0607

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0663

Gnomad OTH AF: 0.0398

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

GnomAD4 genome AF: 0.0418 AC: 6364 AN: 152138 Hom.: 193 Cov.: 32 AF XY: 0.0404 AC XY: 3007 AN XY: 74366

Gnomad4 AFR AF: 0.0108

Gnomad4 AMR AF: 0.0348

Gnomad4 ASJ AF: 0.0130

Gnomad4 EAS AF: 0.00135

Gnomad4 SAS AF: 0.00519

Gnomad4 FIN AF: 0.0607

Gnomad4 NFE AF: 0.0663

Gnomad4 OTH AF: 0.0393

Alfa AF: 0.0534 Hom.: 115

Bravo AF: 0.0393

Asia WGS AF: 0.00347 AC: 12 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	0.62
Dann	Benign	0.92

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: rs11594962; hg19: chr10-105916625;