rs6989157

chr8-95308529-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_038201.1(CFAP418-AS1):n.126+7337G>A variant causes a intron, non coding transcript 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 NR_038201.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0990

Genes affected

CFAP418-AS1 (HGNC:50444): (CFAP418 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CFAP418-AS1	NR_038201.1	n.126+7337G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CFAP418-AS1	ENST00000655917.1	n.56+39639G>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.156

Gnomad4 AMR AF: 0.106

Gnomad4 ASJ AF: 0.135

Gnomad4 EAS AF: 0.00484

Gnomad4 SAS AF: 0.0533

Gnomad4 FIN AF: 0.0724

Gnomad4 NFE AF: 0.133

Gnomad4 OTH AF: 0.140

Alfa AF: 0.132 Hom.: 1837

Bravo AF: 0.130

Asia WGS AF: 0.0470 AC: 166 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	1.9
Dann	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6989157; hg19: chr8-96320757;