rs6989157

Variant names:

• chr8-95308529-G-A
• rs6989157
• ENST00000517437.2:n.78+39639G>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.78+39639G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.125 in 151,966 control chromosomes in the GnomAD database, including 1,244 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 0.13 (1244 hom., cov: 31)
• Consequence: CFAP418-AS1 ENST00000517437.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0990
• 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.152 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.126+7337G>A		intron	N/A
	CFAP418-AS1	NR_038202.1		n.55+39639G>A		intron	N/A
	CFAP418-AS1	NR_038203.1		n.126+7337G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CFAP418-AS1	ENST00000517437.2	TSL:3	n.78+39639G>A		intron	N/A
	CFAP418-AS1	ENST00000517655.1	TSL:4	n.521+103217G>A		intron	N/A
	CFAP418-AS1	ENST00000521905.3	TSL:5	n.149+7337G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.125 AC: 19015 AN: 151848 Hom.: 1239 Cov.: 31

Gnomad AFR AF: 0.155

Gnomad AMI AF: 0.0965

Gnomad AMR AF: 0.106

Gnomad ASJ AF: 0.135

Gnomad EAS AF: 0.00483

Gnomad SAS AF: 0.0535

Gnomad FIN AF: 0.0724

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.133

Gnomad OTH AF: 0.137

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

GnomAD4 genome AF: 0.125 AC: 19049 AN: 151966 Hom.: 1244 Cov.: 31 AF XY: 0.119 AC XY: 8819 AN XY: 74306

African (AFR) AF: 0.156 AC: 6446 AN: 41420

American (AMR) AF: 0.106 AC: 1613 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.135 AC: 467 AN: 3468

East Asian (EAS) AF: 0.00484 AC: 25 AN: 5166

South Asian (SAS) AF: 0.0533 AC: 257 AN: 4822

European-Finnish (FIN) AF: 0.0724 AC: 765 AN: 10570

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.133 AC: 9061 AN: 67940

Other (OTH) AF: 0.140 AC: 296 AN: 2108

Alfa AF: 0.132 Hom.: 2366

Bravo AF: 0.130

Asia WGS AF: 0.0470 AC: 166 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.9
DANN	Benign	0.69
PhyloP100		0.099

Splicing

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

Other links and lift over

dbSNP: rs6989157; hg19: chr8-96320757;