rs2933343

Positions:

• chr3-128939649-G-A
• chr3-128939649-G-C

Variant summary

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

The NM_001394090.1(CFAP92):​c.2259-4330C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.246 in 151,444 control chromosomes in the GnomAD database, including 4,998 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 0.25 (4998 hom., cov: 30)
• Consequence: CFAP92 NM_001394090.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0890

Genes affected

CFAP92 (HGNC:29231): (cilia and flagella associated protein 92 (putative))

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.539 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CFAP92	NM_001394090.1	c.2259-4330C>T		intron_variant		ENST00000645291.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CFAP92	ENST00000645291.3	c.2259-4330C>T		intron_variant			NM_001394090.1	P2
CFAP92	ENST00000511438.5	c.1169-29316C>T		intron_variant		2		A2
CFAP92	ENST00000669741.1	c.69-4330C>T		intron_variant

Frequencies

GnomAD3 genomes AF: 0.246 AC: 37244 AN: 151326 Hom.: 4990 Cov.: 30

Gnomad AFR AF: 0.268

Gnomad AMI AF: 0.146

Gnomad AMR AF: 0.271

Gnomad ASJ AF: 0.277

Gnomad EAS AF: 0.556

Gnomad SAS AF: 0.251

Gnomad FIN AF: 0.170

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.214

Gnomad OTH AF: 0.256

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

GnomAD4 genome AF: 0.246 AC: 37279 AN: 151444 Hom.: 4998 Cov.: 30 AF XY: 0.244 AC XY: 18074 AN XY: 74014

Gnomad4 AFR AF: 0.269

Gnomad4 AMR AF: 0.271

Gnomad4 ASJ AF: 0.277

Gnomad4 EAS AF: 0.556

Gnomad4 SAS AF: 0.252

Gnomad4 FIN AF: 0.170

Gnomad4 NFE AF: 0.214

Gnomad4 OTH AF: 0.254

Alfa AF: 0.219 Hom.: 451

Bravo AF: 0.257

Asia WGS AF: 0.326 AC: 1133 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	4.6
DANN	Benign	0.96

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: rs2933343; hg19: chr3-128658492;