rs4132840

Variant names:

• chr8-95404316-A-G
• rs4132840
• ENST00000517437.2:n.79-28310A>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.79-28310A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0999 in 152,290 control chromosomes in the GnomAD database, including 842 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 0.10 (842 hom., cov: 31)
• Consequence: CFAP418-AS1 ENST00000517437.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.418
• Publications: 2 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.122 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CFAP418-AS1	NR_038201.1	n.127-28310A>G		intron_variant	Intron 2 of 5
CFAP418-AS1	NR_038202.1	n.56-28310A>G		intron_variant	Intron 1 of 4
CFAP418-AS1	NR_038203.1	n.126+103124A>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.79-28310A>G		intron_variant	Intron 1 of 4	3
CFAP418-AS1	ENST00000517655.1	n.522-28310A>G		intron_variant	Intron 2 of 2	4
CFAP418-AS1	ENST00000521905.3	n.150-28310A>G		intron_variant	Intron 2 of 4	5

Frequencies

GnomAD3 genomes AF: 0.0996 AC: 15158 AN: 152172 Hom.: 825 Cov.: 31

Gnomad AFR AF: 0.124

Gnomad AMI AF: 0.0899

Gnomad AMR AF: 0.0903

Gnomad ASJ AF: 0.117

Gnomad EAS AF: 0.0600

Gnomad SAS AF: 0.0997

Gnomad FIN AF: 0.0517

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.0958

Gnomad OTH AF: 0.106

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

GnomAD4 genome AF: 0.0999 AC: 15214 AN: 152290 Hom.: 842 Cov.: 31 AF XY: 0.0974 AC XY: 7255 AN XY: 74466

African (AFR) AF: 0.125 AC: 5183 AN: 41542

American (AMR) AF: 0.0901 AC: 1379 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.117 AC: 407 AN: 3470

East Asian (EAS) AF: 0.0599 AC: 311 AN: 5192

South Asian (SAS) AF: 0.0995 AC: 480 AN: 4822

European-Finnish (FIN) AF: 0.0517 AC: 549 AN: 10620

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.0958 AC: 6518 AN: 68026

Other (OTH) AF: 0.112 AC: 236 AN: 2114

Alfa AF: 0.101 Hom.: 1358

Bravo AF: 0.104

Asia WGS AF: 0.115 AC: 400 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.9
DANN	Benign	0.74
PhyloP100		-0.42

Splicing

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

Other links and lift over

dbSNP: rs4132840; hg19: chr8-96416544;