ENST00000517437.2:n.233+59464A>G

Variant names:

• chr8-95492244-A-G
• rs77742018
• ENST00000517437.2:n.233+59464A>G

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BS1 BS2

The ENST00000517437.2(CFAP418-AS1):​n.233+59464A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.023 in 152,318 control chromosomes in the GnomAD database, including 55 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 0.023 (55 hom., cov: 32)
• Consequence: CFAP418-AS1 ENST00000517437.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.70
• Publications: 3 publications found

Genes affected

CFAP418-AS1 (HGNC:50444): (CFAP418 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.4).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.023 (3502/152318) while in subpopulation NFE AF = 0.036 (2450/68016). AF 95% confidence interval is 0.0348. There are 55 homozygotes in GnomAd4. There are 1667 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 55 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CFAP418-AS1	NR_038201.1	n.281+59464A>G		intron_variant	Intron 3 of 5
CFAP418-AS1	NR_038202.1	n.210+59464A>G		intron_variant	Intron 2 of 4
CFAP418-AS1	NR_038203.1	n.127-118420A>G		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CFAP418-AS1	ENST00000517437.2	n.233+59464A>G		intron_variant	Intron 2 of 4	3
CFAP418-AS1	ENST00000521905.3	n.304+59464A>G		intron_variant	Intron 3 of 4	5
CFAP418-AS1	ENST00000655917.1	n.296+5750A>G		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.0230 AC: 3505 AN: 152200 Hom.: 55 Cov.: 32

Gnomad AFR AF: 0.00764

Gnomad AMI AF: 0.0197

Gnomad AMR AF: 0.0163

Gnomad ASJ AF: 0.0124

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00684

Gnomad FIN AF: 0.0327

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0360

Gnomad OTH AF: 0.0206

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

GnomAD4 genome AF: 0.0230 AC: 3502 AN: 152318 Hom.: 55 Cov.: 32 AF XY: 0.0224 AC XY: 1667 AN XY: 74480

African (AFR) AF: 0.00760 AC: 316 AN: 41592

American (AMR) AF: 0.0163 AC: 250 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0124 AC: 43 AN: 3468

East Asian (EAS) AF: 0.00 AC: 0 AN: 5190

South Asian (SAS) AF: 0.00684 AC: 33 AN: 4822

European-Finnish (FIN) AF: 0.0327 AC: 347 AN: 10616

Middle Eastern (MID) AF: 0.00680 AC: 2 AN: 294

European-Non Finnish (NFE) AF: 0.0360 AC: 2450 AN: 68016

Other (OTH) AF: 0.0203 AC: 43 AN: 2114

Alfa AF: 0.0239 Hom.: 31

Bravo AF: 0.0209

Asia WGS AF: 0.00231 AC: 8 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.40
CADD	Benign	15
DANN	Benign	0.83
PhyloP100		1.7
Mutation Taster		=100/0	polymorphism

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs77742018; hg19: chr8-96504472;