8-95524019-C-T

Position:

• chr8-95524019-C-T

Variant summary

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

The ENST00000517437.1(CFAP418-AS1):​n.145-86645C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.444 in 151,880 control chromosomes in the GnomAD database, including 15,596 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 0.44 (15596 hom., cov: 33)
• Consequence: CFAP418-AS1 ENST00000517437.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.12

Genes affected

CFAP418-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.62).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.498 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CFAP418-AS1	NR_038201.1	n.282-86645C>T		intron_variant
CFAP418-AS1	NR_038202.1	n.211-86645C>T		intron_variant
CFAP418-AS1	NR_038203.1	n.127-86645C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CFAP418-AS1	ENST00000517437.1	n.145-86645C>T		intron_variant		3
ENSG00000253872	ENST00000519366.1	n.269-388C>T		intron_variant		5
CFAP418-AS1	ENST00000521905.2	n.288-86645C>T		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.444 AC: 67354 AN: 151762 Hom.: 15573 Cov.: 33

Gnomad AFR AF: 0.397

Gnomad AMI AF: 0.386

Gnomad AMR AF: 0.431

Gnomad ASJ AF: 0.548

Gnomad EAS AF: 0.0550

Gnomad SAS AF: 0.398

Gnomad FIN AF: 0.453

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.502

Gnomad OTH AF: 0.437

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

GnomAD4 genome AF: 0.444 AC: 67416 AN: 151880 Hom.: 15596 Cov.: 33 AF XY: 0.441 AC XY: 32708 AN XY: 74244

Gnomad4 AFR AF: 0.397

Gnomad4 AMR AF: 0.430

Gnomad4 ASJ AF: 0.548

Gnomad4 EAS AF: 0.0551

Gnomad4 SAS AF: 0.400

Gnomad4 FIN AF: 0.453

Gnomad4 NFE AF: 0.502

Gnomad4 OTH AF: 0.432

Alfa AF: 0.360 Hom.: 987

Bravo AF: 0.435

Asia WGS AF: 0.247 AC: 857 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.62
CADD	Benign	7.5
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2062606; hg19: chr8-96536247;