8-95583508-G-A

Variant names:

• chr8-95583508-G-A
• rs3104964
• ENST00000517437.2:n.234-27156G>A

Variant summary

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

The ENST00000517437.2(CFAP418-AS1):​n.234-27156G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.568 in 152,004 control chromosomes in the GnomAD database, including 24,651 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 0.57 (24651 hom., cov: 33)
• Consequence: CFAP418-AS1 ENST00000517437.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.622
• Publications: 10 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=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.601 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000517437.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CFAP418-AS1	NR_038201.1		n.282-27156G>A		intron	N/A
	CFAP418-AS1	NR_038202.1		n.211-27156G>A		intron	N/A
	CFAP418-AS1	NR_038203.1		n.127-27156G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CFAP418-AS1	ENST00000517437.2	TSL:3	n.234-27156G>A		intron	N/A
	CFAP418-AS1	ENST00000521905.3	TSL:5	n.305-27156G>A		intron	N/A
	CFAP418-AS1	ENST00000655917.1		n.297-27156G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.568 AC: 86234 AN: 151888 Hom.: 24640 Cov.: 33

Gnomad AFR AF: 0.493

Gnomad AMI AF: 0.651

Gnomad AMR AF: 0.573

Gnomad ASJ AF: 0.554

Gnomad EAS AF: 0.521

Gnomad SAS AF: 0.621

Gnomad FIN AF: 0.635

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.601

Gnomad OTH AF: 0.562

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

GnomAD4 genome AF: 0.568 AC: 86279 AN: 152004 Hom.: 24651 Cov.: 33 AF XY: 0.570 AC XY: 42325 AN XY: 74294

African (AFR) AF: 0.494 AC: 20452 AN: 41440

American (AMR) AF: 0.573 AC: 8752 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.554 AC: 1925 AN: 3472

East Asian (EAS) AF: 0.522 AC: 2698 AN: 5166

South Asian (SAS) AF: 0.619 AC: 2986 AN: 4822

European-Finnish (FIN) AF: 0.635 AC: 6711 AN: 10564

Middle Eastern (MID) AF: 0.521 AC: 152 AN: 292

European-Non Finnish (NFE) AF: 0.601 AC: 40827 AN: 67942

Other (OTH) AF: 0.559 AC: 1182 AN: 2116

Alfa AF: 0.575 Hom.: 15523

Bravo AF: 0.558

Asia WGS AF: 0.595 AC: 2069 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	3.2
DANN	Benign	0.18
PhyloP100		0.62

Splicing

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

Other links and lift over

dbSNP: rs3104964; hg19: chr8-96595736;