9-132469020-G-A

Position:

• chr9-132469020-G-A

Variant summary

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

The NM_001282957.2(CFAP77):​c.196-29675G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.531 in 150,894 control chromosomes in the GnomAD database, including 22,744 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 0.53 (22744 hom., cov: 28)
• Consequence: CFAP77 NM_001282957.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.921

Genes affected

CFAP77 (HGNC:33776): (cilia and flagella associated protein 77) Predicted to be located in cilium. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.876 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CFAP77	NM_001282957.2	c.196-29675G>A		intron_variant		ENST00000393216.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CFAP77	ENST00000393216.3	c.196-29675G>A		intron_variant		1	NM_001282957.2	P1
CFAP77	ENST00000343036.6	c.196-13290G>A		intron_variant		2
CFAP77	ENST00000393215.7	c.196-29675G>A		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.532 AC: 80170 AN: 150786 Hom.: 22734 Cov.: 28

Gnomad AFR AF: 0.332

Gnomad AMI AF: 0.559

Gnomad AMR AF: 0.669

Gnomad ASJ AF: 0.553

Gnomad EAS AF: 0.898

Gnomad SAS AF: 0.605

Gnomad FIN AF: 0.671

Gnomad MID AF: 0.467

Gnomad NFE AF: 0.564

Gnomad OTH AF: 0.558

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

GnomAD4 genome AF: 0.531 AC: 80198 AN: 150894 Hom.: 22744 Cov.: 28 AF XY: 0.543 AC XY: 40027 AN XY: 73692

Gnomad4 AFR AF: 0.332

Gnomad4 AMR AF: 0.670

Gnomad4 ASJ AF: 0.553

Gnomad4 EAS AF: 0.897

Gnomad4 SAS AF: 0.605

Gnomad4 FIN AF: 0.671

Gnomad4 NFE AF: 0.564

Gnomad4 OTH AF: 0.557

Alfa AF: 0.567 Hom.: 51235

Bravo AF: 0.526

Asia WGS AF: 0.692 AC: 2405 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.16
DANN	Benign	0.21

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.040		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: rs569434; hg19: chr9-135344407;