10-104167148-T-C

Position:

• chr10-104167148-T-C

Variant summary

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

The NM_025145.7(CFAP43):​c.2809-430A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.222 in 152,172 control chromosomes in the GnomAD database, including 4,120 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 0.22 (4120 hom., cov: 32)
• Consequence: CFAP43 NM_025145.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.35

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=-0.72).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.26 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CFAP43	NM_025145.7	c.2809-430A>G		intron_variant		ENST00000357060.8	NP_079421.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CFAP43	ENST00000357060.8	c.2809-430A>G		intron_variant		1	NM_025145.7	ENSP00000349568	P1
CFAP43	ENST00000434629.5	c.891-430A>G		intron_variant		1		ENSP00000391364

Frequencies

GnomAD3 genomes AF: 0.222 AC: 33794 AN: 152054 Hom.: 4113 Cov.: 32

Gnomad AFR AF: 0.156

Gnomad AMI AF: 0.245

Gnomad AMR AF: 0.212

Gnomad ASJ AF: 0.311

Gnomad EAS AF: 0.119

Gnomad SAS AF: 0.250

Gnomad FIN AF: 0.235

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.263

Gnomad OTH AF: 0.249

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

GnomAD4 genome AF: 0.222 AC: 33816 AN: 152172 Hom.: 4120 Cov.: 32 AF XY: 0.221 AC XY: 16479 AN XY: 74418

Gnomad4 AFR AF: 0.156

Gnomad4 AMR AF: 0.211

Gnomad4 ASJ AF: 0.311

Gnomad4 EAS AF: 0.118

Gnomad4 SAS AF: 0.250

Gnomad4 FIN AF: 0.235

Gnomad4 NFE AF: 0.263

Gnomad4 OTH AF: 0.256

Alfa AF: 0.255 Hom.: 6767

Bravo AF: 0.217

Asia WGS AF: 0.232 AC: 805 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	7.3
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: rs10883974; hg19: chr10-105926906;