3-119764420-G-A

Position:

• chr3-119764420-G-A

Variant summary

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

The NM_033364.4(CFAP91):​c.*2-632G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.339 in 151,984 control chromosomes in the GnomAD database, including 10,514 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 0.34 (10514 hom., cov: 32)
• Consequence: CFAP91 NM_033364.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.556

Genes affected

CFAP91 (HGNC:24010): (cilia and flagella associated protein 91) Predicted to be involved in cilium movement. Predicted to be located in axoneme and motile cilium. Predicted to colocalize with radial spoke stalk. Implicated in spermatogenic failure 51. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000285585 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.445 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CFAP91	NM_033364.4	c.*2-632G>A		intron_variant		ENST00000273390.9	NP_203528.3
CFAP91	NM_001320316.2	c.*2-632G>A		intron_variant			NP_001307245.2
CFAP91	NM_001320317.2	c.*2-632G>A		intron_variant			NP_001307246.2
CFAP91	NM_001320318.2	c.*2-632G>A		intron_variant			NP_001307247.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CFAP91	ENST00000273390.9	c.*2-632G>A		intron_variant		1	NM_033364.4	ENSP00000273390.5
ENSG00000285585	ENST00000648112.1	c.*1+13322G>A		intron_variant				ENSP00000497876.1

Frequencies

GnomAD3 genomes AF: 0.339 AC: 51516 AN: 151866 Hom.: 10514 Cov.: 32

Gnomad AFR AF: 0.0892

Gnomad AMI AF: 0.380

Gnomad AMR AF: 0.428

Gnomad ASJ AF: 0.422

Gnomad EAS AF: 0.374

Gnomad SAS AF: 0.370

Gnomad FIN AF: 0.418

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.449

Gnomad OTH AF: 0.361

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

GnomAD4 genome AF: 0.339 AC: 51524 AN: 151984 Hom.: 10514 Cov.: 32 AF XY: 0.342 AC XY: 25439 AN XY: 74288

Gnomad4 AFR AF: 0.0890

Gnomad4 AMR AF: 0.428

Gnomad4 ASJ AF: 0.422

Gnomad4 EAS AF: 0.373

Gnomad4 SAS AF: 0.372

Gnomad4 FIN AF: 0.418

Gnomad4 NFE AF: 0.449

Gnomad4 OTH AF: 0.365

Alfa AF: 0.438 Hom.: 24037

Bravo AF: 0.329

Asia WGS AF: 0.380 AC: 1323 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.2
DANN	Benign	0.83

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: rs11712308; hg19: chr3-119483267;