rs7021144

chr9-132506811-C-T

Variant summary

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

The NM_001282957.2(CFAP77):c.524+7211C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.196 in 152,024 control chromosomes in the GnomAD database, including 3,120 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 0.20 (3120 hom., cov: 32)
• Consequence: CFAP77 NM_001282957.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.34

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=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.247 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CFAP77	NM_001282957.2	c.524+7211C>T		intron_variant		ENST00000393216.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CFAP77	ENST00000393216.3	c.524+7211C>T		intron_variant		1	NM_001282957.2	P1
CFAP77	ENST00000343036.6	c.632+7211C>T		intron_variant		2
CFAP77	ENST00000393215.7	c.525-6448C>T		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.196 AC: 29743 AN: 151906 Hom.: 3116 Cov.: 32

Gnomad AFR AF: 0.251

Gnomad AMI AF: 0.321

Gnomad AMR AF: 0.147

Gnomad ASJ AF: 0.0982

Gnomad EAS AF: 0.0846

Gnomad SAS AF: 0.161

Gnomad FIN AF: 0.104

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.202

Gnomad OTH AF: 0.179

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

GnomAD4 genome AF: 0.196 AC: 29750 AN: 152024 Hom.: 3120 Cov.: 32 AF XY: 0.189 AC XY: 14053 AN XY: 74330

Gnomad4 AFR AF: 0.251

Gnomad4 AMR AF: 0.147

Gnomad4 ASJ AF: 0.0982

Gnomad4 EAS AF: 0.0845

Gnomad4 SAS AF: 0.160

Gnomad4 FIN AF: 0.104

Gnomad4 NFE AF: 0.202

Gnomad4 OTH AF: 0.177

Alfa AF: 0.195 Hom.: 4093

Bravo AF: 0.205

Asia WGS AF: 0.131 AC: 457 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	7.6
Dann	Benign	0.67

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: rs7021144; hg19: chr9-135382198; COSMIC: COSV58008959;