rs10512711

Positions:

• chr3-128968765-G-A

Variant summary

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

The ENST00000265068.9(CFAP92):​c.*2460C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0722 in 152,404 control chromosomes in the GnomAD database, including 1,032 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 0.072 (1031 hom., cov: 32)
  • Exomes 𝑓: 0.017 (1 hom.)
• Consequence: CFAP92 ENST00000265068.9 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.357

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=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.212 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CFAP92	NM_001394090.1	c.1168+2522C>T		intron_variant		ENST00000645291.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CFAP92	ENST00000265068.9	c.*2460C>T		3_prime_UTR_variant	8/8	1		A2
CFAP92	ENST00000645291.3	c.1168+2522C>T		intron_variant			NM_001394090.1	P2
CFAP92	ENST00000511438.5	c.1168+2522C>T		intron_variant		2		A2

Frequencies

GnomAD3 genomes AF: 0.0722 AC: 10993 AN: 152170 Hom.: 1028 Cov.: 32

Gnomad AFR AF: 0.216

Gnomad AMI AF: 0.00768

Gnomad AMR AF: 0.0344

Gnomad ASJ AF: 0.0222

Gnomad EAS AF: 0.0473

Gnomad SAS AF: 0.107

Gnomad FIN AF: 0.0240

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.00441

Gnomad OTH AF: 0.0517

GnomAD4 exome AF: 0.0172 AC: 2 AN: 116 Hom.: 1 Cov.: 0 AF XY: 0.0278 AC XY: 2 AN XY: 72

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.0723 AC: 11006 AN: 152288 Hom.: 1031 Cov.: 32 AF XY: 0.0720 AC XY: 5359 AN XY: 74448

Gnomad4 AFR AF: 0.216

Gnomad4 AMR AF: 0.0344

Gnomad4 ASJ AF: 0.0222

Gnomad4 EAS AF: 0.0472

Gnomad4 SAS AF: 0.107

Gnomad4 FIN AF: 0.0240

Gnomad4 NFE AF: 0.00441

Gnomad4 OTH AF: 0.0507

Alfa AF: 0.0141 Hom.: 193

Bravo AF: 0.0784

Asia WGS AF: 0.0880 AC: 308 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.26
DANN	Benign	0.44

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: rs10512711; hg19: chr3-128687608;