chr3-128968765-G-A

Variant names:

• chr3-128968765-G-A
• rs10512711
• ENST00000265068.9:c.*2460C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 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=-0.98).
• 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 rank	MANE	Protein	UniProt
CFAP92	NM_001394090.1	c.1168+2522C>T		intron_variant	Intron 8 of 15	ENST00000645291.3	NP_001381019.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CFAP92	ENST00000265068.9	c.*2460C>T		3_prime_UTR_variant	Exon 8 of 8	1		ENSP00000265068.5
CFAP92	ENST00000645291.3	c.1168+2522C>T		intron_variant	Intron 8 of 15		NM_001394090.1	ENSP00000496592.2
CFAP92	ENST00000511438.5	c.1168+2522C>T		intron_variant	Intron 7 of 7	2		ENSP00000426217.1

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

African (AFR) AF: 0.00 AC: 0 AN: 4

American (AMR) AF: 0.00 AC: 0 AN: 4

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.00 AC: 0 AN: 6

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 18

Middle Eastern (MID) AF: 1.00 AC: 2 AN: 2

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 74

Other (OTH) AF: 0.00 AC: 0 AN: 8

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

African (AFR) AF: 0.216 AC: 8966 AN: 41546

American (AMR) AF: 0.0344 AC: 527 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.0222 AC: 77 AN: 3470

East Asian (EAS) AF: 0.0472 AC: 245 AN: 5188

South Asian (SAS) AF: 0.107 AC: 514 AN: 4824

European-Finnish (FIN) AF: 0.0240 AC: 254 AN: 10604

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.00441 AC: 300 AN: 68032

Other (OTH) AF: 0.0507 AC: 107 AN: 2112

Alfa AF: 0.0252 Hom.: 1148

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
PhyloP100		-0.36
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: rs10512711; hg19: chr3-128687608;