rs894151

Variant names:

• chr8-95226180-T-C
• rs894151
• ENST00000517655.1:n.521+20868T>C

Variant summary

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

The ENST00000517655.1(CFAP418-AS1):​n.521+20868T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.394 in 152,164 control chromosomes in the GnomAD database, including 12,618 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 0.39 (12618 hom., cov: 32)
• Consequence: CFAP418-AS1 ENST00000517655.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.99

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=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.498 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CFAP418-AS1	ENST00000517655.1	n.521+20868T>C		intron_variant	Intron 2 of 2	4

Frequencies

GnomAD3 genomes AF: 0.394 AC: 59961 AN: 152044 Hom.: 12600 Cov.: 32

Gnomad AFR AF: 0.271

Gnomad AMI AF: 0.570

Gnomad AMR AF: 0.347

Gnomad ASJ AF: 0.453

Gnomad EAS AF: 0.200

Gnomad SAS AF: 0.514

Gnomad FIN AF: 0.430

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.475

Gnomad OTH AF: 0.402

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

GnomAD4 genome AF: 0.394 AC: 60016 AN: 152164 Hom.: 12618 Cov.: 32 AF XY: 0.392 AC XY: 29190 AN XY: 74386

Gnomad4 AFR AF: 0.271

Gnomad4 AMR AF: 0.347

Gnomad4 ASJ AF: 0.453

Gnomad4 EAS AF: 0.200

Gnomad4 SAS AF: 0.515

Gnomad4 FIN AF: 0.430

Gnomad4 NFE AF: 0.475

Gnomad4 OTH AF: 0.409

Alfa AF: 0.452 Hom.: 15496

Bravo AF: 0.378

Asia WGS AF: 0.354 AC: 1234 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.013
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs894151; hg19: chr8-96238408;