rs6471542

chr8-95543831-C-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.282-66833C>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 0.622 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 NR_038201.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.119

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=-0.95).
• 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/exons	MANE	UniProt
CFAP418-AS1	NR_038201.1	n.282-66833C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CFAP418-AS1	ENST00000655917.1	n.296+57337C>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.610

Gnomad4 AMR AF: 0.510

Gnomad4 ASJ AF: 0.651

Gnomad4 EAS AF: 0.278

Gnomad4 SAS AF: 0.486

Gnomad4 FIN AF: 0.725

Gnomad4 NFE AF: 0.671

Gnomad4 OTH AF: 0.607

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6471542; hg19: chr8-96556059;