3-128933710-C-T

Position:

• chr3-128933710-C-T

Variant summary

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

The NM_001394090.1(CFAP92):​c.2454-713G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.127 in 152,194 control chromosomes in the GnomAD database, including 1,936 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 0.13 (1936 hom., cov: 33)
• Consequence: CFAP92 NM_001394090.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00400

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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.273 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CFAP92	NM_001394090.1	c.2454-713G>A		intron_variant		ENST00000645291.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CFAP92	ENST00000645291.3	c.2454-713G>A		intron_variant			NM_001394090.1	P2
CFAP92	ENST00000511438.5	c.1169-23377G>A		intron_variant		2		A2
CFAP92	ENST00000637488.2	c.34-713G>A		intron_variant		5
CFAP92	ENST00000669741.1	c.264-713G>A		intron_variant

Frequencies

GnomAD3 genomes AF: 0.127 AC: 19315 AN: 152076 Hom.: 1934 Cov.: 33

Gnomad AFR AF: 0.278

Gnomad AMI AF: 0.0626

Gnomad AMR AF: 0.101

Gnomad ASJ AF: 0.110

Gnomad EAS AF: 0.00135

Gnomad SAS AF: 0.0182

Gnomad FIN AF: 0.0682

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0696

Gnomad OTH AF: 0.124

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

GnomAD4 genome AF: 0.127 AC: 19341 AN: 152194 Hom.: 1936 Cov.: 33 AF XY: 0.125 AC XY: 9285 AN XY: 74414

Gnomad4 AFR AF: 0.278

Gnomad4 AMR AF: 0.101

Gnomad4 ASJ AF: 0.110

Gnomad4 EAS AF: 0.00135

Gnomad4 SAS AF: 0.0184

Gnomad4 FIN AF: 0.0682

Gnomad4 NFE AF: 0.0696

Gnomad4 OTH AF: 0.124

Alfa AF: 0.0784 Hom.: 1253

Bravo AF: 0.138

Asia WGS AF: 0.0300 AC: 106 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.71
DANN	Benign	0.74

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: rs9810890; hg19: chr3-128652553;