9-132469020-G-A

Variant names:

• chr9-132469020-G-A
• rs569434
• NM_001282957.2:c.196-29675G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 9 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001282957.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CFAP77	NM_001282957.2	MANE Select	c.196-29675G>A		intron	N/A	NP_001269886.1
	CFAP77	NM_207417.3		c.196-13290G>A		intron	N/A	NP_997300.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CFAP77	ENST00000393216.3	TSL:1 MANE Select	c.196-29675G>A		intron	N/A	ENSP00000376909.2
	CFAP77	ENST00000343036.6	TSL:2	c.196-13290G>A		intron	N/A	ENSP00000343290.2
	CFAP77	ENST00000393215.7	TSL:5	c.196-29675G>A		intron	N/A	ENSP00000376908.3

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

African (AFR) AF: 0.332 AC: 13548 AN: 40810

American (AMR) AF: 0.670 AC: 10147 AN: 15148

Ashkenazi Jewish (ASJ) AF: 0.553 AC: 1918 AN: 3470

East Asian (EAS) AF: 0.897 AC: 4617 AN: 5146

South Asian (SAS) AF: 0.605 AC: 2889 AN: 4778

European-Finnish (FIN) AF: 0.671 AC: 6994 AN: 10420

Middle Eastern (MID) AF: 0.475 AC: 135 AN: 284

European-Non Finnish (NFE) AF: 0.564 AC: 38278 AN: 67838

Other (OTH) AF: 0.557 AC: 1168 AN: 2098

Alfa AF: 0.561 Hom.: 108578

Bravo AF: 0.526

Asia WGS AF: 0.692 AC: 2405 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.16
DANN	Benign	0.21
PhyloP100		-0.92
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs569434; hg19: chr9-135344407;