8-95524019-C-T

Variant names:

• chr8-95524019-C-T
• rs2062606
• ENST00000517437.2:n.234-86645C>T

Variant summary

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

The ENST00000517437.2(CFAP418-AS1):​n.234-86645C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.444 in 151,880 control chromosomes in the GnomAD database, including 15,596 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 0.44 (15596 hom., cov: 33)
• Consequence: CFAP418-AS1 ENST00000517437.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.12
• 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=-0.62).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.498 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.282-86645C>T		intron	N/A
	CFAP418-AS1	NR_038202.1		n.211-86645C>T		intron	N/A
	CFAP418-AS1	NR_038203.1		n.127-86645C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CFAP418-AS1	ENST00000517437.2	TSL:3	n.234-86645C>T		intron	N/A
	CFAP418-AS1	ENST00000519366.1	TSL:5	n.269-388C>T		intron	N/A
	CFAP418-AS1	ENST00000521905.3	TSL:5	n.305-86645C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.444 AC: 67354 AN: 151762 Hom.: 15573 Cov.: 33

Gnomad AFR AF: 0.397

Gnomad AMI AF: 0.386

Gnomad AMR AF: 0.431

Gnomad ASJ AF: 0.548

Gnomad EAS AF: 0.0550

Gnomad SAS AF: 0.398

Gnomad FIN AF: 0.453

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.502

Gnomad OTH AF: 0.437

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

GnomAD4 genome AF: 0.444 AC: 67416 AN: 151880 Hom.: 15596 Cov.: 33 AF XY: 0.441 AC XY: 32708 AN XY: 74244

African (AFR) AF: 0.397 AC: 16438 AN: 41366

American (AMR) AF: 0.430 AC: 6562 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.548 AC: 1900 AN: 3468

East Asian (EAS) AF: 0.0551 AC: 285 AN: 5174

South Asian (SAS) AF: 0.400 AC: 1925 AN: 4818

European-Finnish (FIN) AF: 0.453 AC: 4769 AN: 10534

Middle Eastern (MID) AF: 0.480 AC: 141 AN: 294

European-Non Finnish (NFE) AF: 0.502 AC: 34136 AN: 67954

Other (OTH) AF: 0.432 AC: 909 AN: 2106

Alfa AF: 0.360 Hom.: 987

Bravo AF: 0.435

Asia WGS AF: 0.247 AC: 857 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.62
CADD	Benign	7.5
DANN	Benign	0.48
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs2062606; hg19: chr8-96536247;