rs515910

Positions:

• chr10-104206646-A-G

Variant summary

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

The NM_025145.7(CFAP43):​c.896-616T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.471 in 152,032 control chromosomes in the GnomAD database, including 17,787 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 0.47 (17787 hom., cov: 31)
• Consequence: CFAP43 NM_025145.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.790

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=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.645 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CFAP43	NM_025145.7	c.896-616T>C		intron_variant		ENST00000357060.8	NP_079421.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CFAP43	ENST00000357060.8	c.896-616T>C		intron_variant		1	NM_025145.7	ENSP00000349568.3
CFAP43	ENST00000278064.7	c.896-613T>C		intron_variant		1		ENSP00000278064.3
CFAP43	ENST00000369720.6	c.896-613T>C		intron_variant		1		ENSP00000358734.2
CFAP43	ENST00000369719.2	c.896-613T>C		intron_variant		2		ENSP00000358733.2

Frequencies

GnomAD3 genomes AF: 0.471 AC: 71481 AN: 151914 Hom.: 17743 Cov.: 31

Gnomad AFR AF: 0.651

Gnomad AMI AF: 0.341

Gnomad AMR AF: 0.413

Gnomad ASJ AF: 0.414

Gnomad EAS AF: 0.386

Gnomad SAS AF: 0.515

Gnomad FIN AF: 0.365

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.399

Gnomad OTH AF: 0.452

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

GnomAD4 genome AF: 0.471 AC: 71579 AN: 152032 Hom.: 17787 Cov.: 31 AF XY: 0.470 AC XY: 34939 AN XY: 74304

Gnomad4 AFR AF: 0.652

Gnomad4 AMR AF: 0.412

Gnomad4 ASJ AF: 0.414

Gnomad4 EAS AF: 0.386

Gnomad4 SAS AF: 0.515

Gnomad4 FIN AF: 0.365

Gnomad4 NFE AF: 0.399

Gnomad4 OTH AF: 0.455

Alfa AF: 0.414 Hom.: 16913

Bravo AF: 0.478

Asia WGS AF: 0.508 AC: 1766 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.81
DANN	Benign	0.77

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: rs515910; hg19: chr10-105966404;