rs1680786

Positions:

• chr3-128925997-T-C

Variant summary

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

The NM_001394090.1(CFAP92):​c.2751+6703A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.433 in 151,996 control chromosomes in the GnomAD database, including 16,744 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 0.43 (16744 hom., cov: 33)
• Consequence: CFAP92 NM_001394090.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.726

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=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.695 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CFAP92	NM_001394090.1	c.2751+6703A>G		intron_variant		ENST00000645291.3	NP_001381019.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CFAP92	ENST00000645291.3	c.2751+6703A>G		intron_variant			NM_001394090.1	ENSP00000496592.2
CFAP92	ENST00000511438.5	c.1169-15664A>G		intron_variant		2		ENSP00000426217.1
CFAP92	ENST00000669741.1	c.561+6703A>G		intron_variant				ENSP00000499631.1
CFAP92	ENST00000637488.2	c.330+6703A>G		intron_variant		5		ENSP00000490565.2

Frequencies

GnomAD3 genomes AF: 0.433 AC: 65719 AN: 151878 Hom.: 16710 Cov.: 33

Gnomad AFR AF: 0.702

Gnomad AMI AF: 0.207

Gnomad AMR AF: 0.400

Gnomad ASJ AF: 0.404

Gnomad EAS AF: 0.639

Gnomad SAS AF: 0.382

Gnomad FIN AF: 0.275

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.294

Gnomad OTH AF: 0.422

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

GnomAD4 genome AF: 0.433 AC: 65804 AN: 151996 Hom.: 16744 Cov.: 33 AF XY: 0.430 AC XY: 31926 AN XY: 74316

Gnomad4 AFR AF: 0.702

Gnomad4 AMR AF: 0.400

Gnomad4 ASJ AF: 0.404

Gnomad4 EAS AF: 0.638

Gnomad4 SAS AF: 0.382

Gnomad4 FIN AF: 0.275

Gnomad4 NFE AF: 0.294

Gnomad4 OTH AF: 0.421

Alfa AF: 0.369 Hom.: 1519

Bravo AF: 0.457

Asia WGS AF: 0.475 AC: 1652 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	4.9
DANN	Benign	0.82

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: rs1680786; hg19: chr3-128644840;