8-95673067-A-G

Variant names:

• chr8-95673067-A-G
• rs7013599
• ENST00000517437.2:n.267+62370A>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.267+62370A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.422 in 152,078 control chromosomes in the GnomAD database, including 14,093 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 0.42 (14093 hom., cov: 32)
• Consequence: CFAP418-AS1 ENST00000517437.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.760
• Publications: 3 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=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.484 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CFAP418-AS1	NR_038201.1		n.315+62370A>G		intron	N/A
	CFAP418-AS1	NR_038202.1		n.244+62370A>G		intron	N/A
	CFAP418-AS1	NR_038203.1		n.160+62370A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CFAP418-AS1	ENST00000517437.2	TSL:3	n.267+62370A>G		intron	N/A
	CFAP418-AS1	ENST00000655917.1		n.330+62370A>G		intron	N/A
	CFAP418-AS1	ENST00000664790.1		n.34+62370A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.422 AC: 64194 AN: 151960 Hom.: 14095 Cov.: 32

Gnomad AFR AF: 0.311

Gnomad AMI AF: 0.392

Gnomad AMR AF: 0.457

Gnomad ASJ AF: 0.473

Gnomad EAS AF: 0.305

Gnomad SAS AF: 0.337

Gnomad FIN AF: 0.456

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.489

Gnomad OTH AF: 0.455

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

GnomAD4 genome AF: 0.422 AC: 64217 AN: 152078 Hom.: 14093 Cov.: 32 AF XY: 0.420 AC XY: 31239 AN XY: 74348

African (AFR) AF: 0.311 AC: 12925 AN: 41512

American (AMR) AF: 0.457 AC: 6979 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.473 AC: 1641 AN: 3470

East Asian (EAS) AF: 0.306 AC: 1580 AN: 5170

South Asian (SAS) AF: 0.336 AC: 1621 AN: 4818

European-Finnish (FIN) AF: 0.456 AC: 4819 AN: 10558

Middle Eastern (MID) AF: 0.466 AC: 137 AN: 294

European-Non Finnish (NFE) AF: 0.489 AC: 33212 AN: 67954

Other (OTH) AF: 0.450 AC: 946 AN: 2104

Alfa AF: 0.465 Hom.: 65606

Bravo AF: 0.420

Asia WGS AF: 0.338 AC: 1178 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.28
DANN	Benign	0.54
PhyloP100		-0.76

Splicing

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

Other links and lift over

dbSNP: rs7013599; hg19: chr8-96685295;