rs1909881

Variant names:

• chr8-95503660-A-G
• rs1909881
• ENST00000517437.2:n.233+70880A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000517437.2(CFAP418-AS1):​n.233+70880A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.151 in 152,008 control chromosomes in the GnomAD database, including 1,804 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 0.15 (1804 hom., cov: 32)
• Consequence: CFAP418-AS1 ENST00000517437.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.08
• Publications: 5 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.169 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CFAP418-AS1	NR_038201.1	n.281+70880A>G		intron_variant	Intron 3 of 5
CFAP418-AS1	NR_038202.1	n.210+70880A>G		intron_variant	Intron 2 of 4
CFAP418-AS1	NR_038203.1	n.127-107004A>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+70880A>G		intron_variant	Intron 2 of 4	3
CFAP418-AS1	ENST00000521905.3	n.304+70880A>G		intron_variant	Intron 3 of 4	5
CFAP418-AS1	ENST00000655917.1	n.296+17166A>G		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.151 AC: 22885 AN: 151890 Hom.: 1804 Cov.: 32

Gnomad AFR AF: 0.172

Gnomad AMI AF: 0.163

Gnomad AMR AF: 0.100

Gnomad ASJ AF: 0.0878

Gnomad EAS AF: 0.172

Gnomad SAS AF: 0.134

Gnomad FIN AF: 0.207

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.143

Gnomad OTH AF: 0.127

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

GnomAD4 genome AF: 0.151 AC: 22901 AN: 152008 Hom.: 1804 Cov.: 32 AF XY: 0.153 AC XY: 11370 AN XY: 74312

African (AFR) AF: 0.172 AC: 7132 AN: 41400

American (AMR) AF: 0.100 AC: 1528 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.0878 AC: 305 AN: 3472

East Asian (EAS) AF: 0.172 AC: 891 AN: 5186

South Asian (SAS) AF: 0.135 AC: 648 AN: 4814

European-Finnish (FIN) AF: 0.207 AC: 2191 AN: 10574

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.143 AC: 9753 AN: 67976

Other (OTH) AF: 0.128 AC: 270 AN: 2108

Alfa AF: 0.141 Hom.: 5062

Bravo AF: 0.141

Asia WGS AF: 0.160 AC: 556 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	7.0
DANN	Benign	0.49
PhyloP100		1.1
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs1909881; hg19: chr8-96515888;