rs1203791

chr4-2420546-C-T

Variant summary

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

The ENST00000635017.2(CFAP99):c.-18+1453C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.163 in 152,080 control chromosomes in the GnomAD database, including 2,178 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 0.16 (2178 hom., cov: 32)
• Consequence: CFAP99 ENST00000635017.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0790

Genes affected

CFAP99 (HGNC:51180): (cilia and flagella associated protein 99) Predicted to be located in motile 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.323 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CFAP99	NM_001193282.4	c.-18+1453C>T		intron_variant		ENST00000635017.2
CFAP99	XM_047415685.1	c.-18+1453C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CFAP99	ENST00000635017.2	c.-18+1453C>T		intron_variant		5	NM_001193282.4	P1
CFAP99	ENST00000382849.2	n.120+1453C>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.163 AC: 24707 AN: 151962 Hom.: 2172 Cov.: 32

Gnomad AFR AF: 0.130

Gnomad AMI AF: 0.159

Gnomad AMR AF: 0.170

Gnomad ASJ AF: 0.125

Gnomad EAS AF: 0.335

Gnomad SAS AF: 0.237

Gnomad FIN AF: 0.196

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.159

Gnomad OTH AF: 0.175

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

GnomAD4 genome AF: 0.163 AC: 24725 AN: 152080 Hom.: 2178 Cov.: 32 AF XY: 0.167 AC XY: 12407 AN XY: 74354

Gnomad4 AFR AF: 0.130

Gnomad4 AMR AF: 0.170

Gnomad4 ASJ AF: 0.125

Gnomad4 EAS AF: 0.336

Gnomad4 SAS AF: 0.238

Gnomad4 FIN AF: 0.196

Gnomad4 NFE AF: 0.158

Gnomad4 OTH AF: 0.178

Alfa AF: 0.161 Hom.: 1142

Bravo AF: 0.160

Asia WGS AF: 0.303 AC: 1055 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	4.8
Dann	Benign	0.27

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: rs1203791; hg19: chr4-2422273;