rs6471542

Variant names:

• chr8-95543831-C-A
• rs6471542
• ENST00000517437.2:n.234-66833C>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.234-66833C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.622 in 152,062 control chromosomes in the GnomAD database, including 30,169 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 0.62 (30169 hom., cov: 33)
• Consequence: CFAP418-AS1 ENST00000517437.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.119
• 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=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.666 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CFAP418-AS1	NR_038201.1	n.282-66833C>A		intron_variant	Intron 3 of 5
CFAP418-AS1	NR_038202.1	n.211-66833C>A		intron_variant	Intron 2 of 4
CFAP418-AS1	NR_038203.1	n.127-66833C>A		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CFAP418-AS1	ENST00000517437.2	n.234-66833C>A		intron_variant	Intron 2 of 4	3
CFAP418-AS1	ENST00000521905.3	n.305-66833C>A		intron_variant	Intron 3 of 4	5
CFAP418-AS1	ENST00000655917.1	n.296+57337C>A		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.622 AC: 94474 AN: 151942 Hom.: 30146 Cov.: 33

Gnomad AFR AF: 0.610

Gnomad AMI AF: 0.715

Gnomad AMR AF: 0.511

Gnomad ASJ AF: 0.651

Gnomad EAS AF: 0.279

Gnomad SAS AF: 0.486

Gnomad FIN AF: 0.725

Gnomad MID AF: 0.706

Gnomad NFE AF: 0.671

Gnomad OTH AF: 0.610

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

GnomAD4 genome AF: 0.622 AC: 94535 AN: 152062 Hom.: 30169 Cov.: 33 AF XY: 0.618 AC XY: 45901 AN XY: 74330

African (AFR) AF: 0.610 AC: 25305 AN: 41492

American (AMR) AF: 0.510 AC: 7779 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.651 AC: 2258 AN: 3466

East Asian (EAS) AF: 0.278 AC: 1440 AN: 5174

South Asian (SAS) AF: 0.486 AC: 2346 AN: 4826

European-Finnish (FIN) AF: 0.725 AC: 7652 AN: 10560

Middle Eastern (MID) AF: 0.728 AC: 214 AN: 294

European-Non Finnish (NFE) AF: 0.671 AC: 45609 AN: 67970

Other (OTH) AF: 0.607 AC: 1280 AN: 2110

Alfa AF: 0.629 Hom.: 4900

Bravo AF: 0.605

Asia WGS AF: 0.412 AC: 1436 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.28
DANN	Benign	0.44
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs6471542; hg19: chr8-96556059;