rs1203791

Variant names:

• chr4-2420546-C-T
• rs1203791
• ENST00000635017.2:c.-18+1453C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
CFAP99	NM_001193282.4	c.-18+1453C>T		intron_variant	Intron 1 of 15		NP_001180211.2
CFAP99	XM_047415685.1	c.-18+1453C>T		intron_variant	Intron 1 of 14		XP_047271641.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CFAP99	ENST00000635017.2	c.-18+1453C>T		intron_variant	Intron 1 of 15	5		ENSP00000488922.2
CFAP99	ENST00000382849.2	n.120+1453C>T		intron_variant	Intron 1 of 2	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

African (AFR) AF: 0.130 AC: 5388 AN: 41482

American (AMR) AF: 0.170 AC: 2592 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.125 AC: 434 AN: 3470

East Asian (EAS) AF: 0.336 AC: 1735 AN: 5160

South Asian (SAS) AF: 0.238 AC: 1144 AN: 4816

European-Finnish (FIN) AF: 0.196 AC: 2076 AN: 10584

Middle Eastern (MID) AF: 0.201 AC: 59 AN: 294

European-Non Finnish (NFE) AF: 0.158 AC: 10776 AN: 67988

Other (OTH) AF: 0.178 AC: 376 AN: 2116

Alfa AF: 0.160 Hom.: 1264

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
PhyloP100		0.079

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

Other links and lift over

dbSNP: rs1203791; hg19: chr4-2422273;