NM_001394090.1:c.2454-713G>A

Variant names:

• chr3-128933710-C-T
• rs9810890
• NM_001394090.1:c.2454-713G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 12 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
CFAP92	NM_001394090.1	c.2454-713G>A		intron_variant	Intron 11 of 15	ENST00000645291.3	NP_001381019.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CFAP92	ENST00000645291.3	c.2454-713G>A		intron_variant	Intron 11 of 15		NM_001394090.1	ENSP00000496592.2
CFAP92	ENST00000511438.5	c.1169-23377G>A		intron_variant	Intron 7 of 7	2		ENSP00000426217.1
CFAP92	ENST00000669741.1	c.264-713G>A		intron_variant	Intron 2 of 4			ENSP00000499631.1
CFAP92	ENST00000637488.2	c.33-713G>A		intron_variant	Intron 1 of 5	5		ENSP00000490565.2

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

African (AFR) AF: 0.278 AC: 11515 AN: 41478

American (AMR) AF: 0.101 AC: 1549 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.110 AC: 382 AN: 3470

East Asian (EAS) AF: 0.00135 AC: 7 AN: 5188

South Asian (SAS) AF: 0.0184 AC: 89 AN: 4830

European-Finnish (FIN) AF: 0.0682 AC: 723 AN: 10608

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.0696 AC: 4736 AN: 68006

Other (OTH) AF: 0.124 AC: 261 AN: 2112

Alfa AF: 0.0910 Hom.: 2902

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
PhyloP100		-0.0040
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs9810890; hg19: chr3-128652553;