rs4132840

chr8-95404316-A-G

Variant summary

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

The NR_038201.1(CFAP418-AS1):n.127-28310A>G 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 0.0999 in 152,290 control chromosomes in the GnomAD database, including 842 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 0.10 (842 hom., cov: 31)
• Consequence: CFAP418-AS1 NR_038201.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.418

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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.122 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CFAP418-AS1	NR_038201.1	n.127-28310A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CFAP418-AS1	ENST00000655917.1	n.57-28310A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0996 AC: 15158 AN: 152172 Hom.: 825 Cov.: 31

Gnomad AFR AF: 0.124

Gnomad AMI AF: 0.0899

Gnomad AMR AF: 0.0903

Gnomad ASJ AF: 0.117

Gnomad EAS AF: 0.0600

Gnomad SAS AF: 0.0997

Gnomad FIN AF: 0.0517

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.0958

Gnomad OTH AF: 0.106

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

GnomAD4 genome AF: 0.0999 AC: 15214 AN: 152290 Hom.: 842 Cov.: 31 AF XY: 0.0974 AC XY: 7255 AN XY: 74466

Gnomad4 AFR AF: 0.125

Gnomad4 AMR AF: 0.0901

Gnomad4 ASJ AF: 0.117

Gnomad4 EAS AF: 0.0599

Gnomad4 SAS AF: 0.0995

Gnomad4 FIN AF: 0.0517

Gnomad4 NFE AF: 0.0958

Gnomad4 OTH AF: 0.112

Alfa AF: 0.100 Hom.: 1059

Bravo AF: 0.104

Asia WGS AF: 0.115 AC: 400 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	1.9
Dann	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4132840; hg19: chr8-96416544;