8-95529732-C-G

Variant names:

• chr8-95529732-C-G
• rs1500911
• ENST00000517437.2:n.234-80932C>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.234-80932C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.648 in 151,948 control chromosomes in the GnomAD database, including 32,251 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 0.65 (32251 hom., cov: 32)
• Consequence: CFAP418-AS1 ENST00000517437.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04
• Publications: 1 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=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.789 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CFAP418-AS1	NR_038201.1	n.282-80932C>G		intron_variant	Intron 3 of 5
CFAP418-AS1	NR_038202.1	n.211-80932C>G		intron_variant	Intron 2 of 4
CFAP418-AS1	NR_038203.1	n.127-80932C>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.234-80932C>G		intron_variant	Intron 2 of 4	3
CFAP418-AS1	ENST00000521905.3	n.305-80932C>G		intron_variant	Intron 3 of 4	5
CFAP418-AS1	ENST00000655917.1	n.296+43238C>G		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.648 AC: 98398 AN: 151830 Hom.: 32210 Cov.: 32

Gnomad AFR AF: 0.710

Gnomad AMI AF: 0.458

Gnomad AMR AF: 0.667

Gnomad ASJ AF: 0.609

Gnomad EAS AF: 0.808

Gnomad SAS AF: 0.790

Gnomad FIN AF: 0.567

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.602

Gnomad OTH AF: 0.622

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

GnomAD4 genome AF: 0.648 AC: 98498 AN: 151948 Hom.: 32251 Cov.: 32 AF XY: 0.652 AC XY: 48418 AN XY: 74246

African (AFR) AF: 0.710 AC: 29423 AN: 41446

American (AMR) AF: 0.667 AC: 10184 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.609 AC: 2113 AN: 3468

East Asian (EAS) AF: 0.809 AC: 4191 AN: 5180

South Asian (SAS) AF: 0.790 AC: 3804 AN: 4814

European-Finnish (FIN) AF: 0.567 AC: 5979 AN: 10542

Middle Eastern (MID) AF: 0.578 AC: 170 AN: 294

European-Non Finnish (NFE) AF: 0.602 AC: 40901 AN: 67930

Other (OTH) AF: 0.626 AC: 1317 AN: 2104

Alfa AF: 0.642 Hom.: 3891

Bravo AF: 0.654

Asia WGS AF: 0.787 AC: 2730 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.81
DANN	Benign	0.18
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs1500911; hg19: chr8-96541960; COSMIC: COSV107542023;