rs7836535

Positions:

• chr8-95693344-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.178+82647C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.245 in 152,004 control chromosomes in the GnomAD database, including 5,026 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 0.24 (5026 hom., cov: 32)
• Consequence: CFAP418-AS1 ENST00000517437.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.483

Genes affected

CFAP418-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.45 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CFAP418-AS1	NR_038201.1	n.315+82647C>T		intron_variant
CFAP418-AS1	NR_038202.1	n.244+82647C>T		intron_variant
CFAP418-AS1	NR_038203.1	n.160+82647C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CFAP418-AS1	ENST00000517437.1	n.178+82647C>T		intron_variant		3
CFAP418-AS1	ENST00000655917.1	n.330+82647C>T		intron_variant
CFAP418-AS1	ENST00000664790.1	n.34+82647C>T		intron_variant
CFAP418-AS1	ENST00000671532.1	n.257+82647C>T		intron_variant

Frequencies

GnomAD3 genomes AF: 0.245 AC: 37160 AN: 151886 Hom.: 5003 Cov.: 32

Gnomad AFR AF: 0.293

Gnomad AMI AF: 0.183

Gnomad AMR AF: 0.274

Gnomad ASJ AF: 0.221

Gnomad EAS AF: 0.466

Gnomad SAS AF: 0.417

Gnomad FIN AF: 0.180

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.192

Gnomad OTH AF: 0.246

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

GnomAD4 genome AF: 0.245 AC: 37221 AN: 152004 Hom.: 5026 Cov.: 32 AF XY: 0.249 AC XY: 18483 AN XY: 74326

Gnomad4 AFR AF: 0.293

Gnomad4 AMR AF: 0.275

Gnomad4 ASJ AF: 0.221

Gnomad4 EAS AF: 0.465

Gnomad4 SAS AF: 0.419

Gnomad4 FIN AF: 0.180

Gnomad4 NFE AF: 0.192

Gnomad4 OTH AF: 0.253

Alfa AF: 0.215 Hom.: 1760

Bravo AF: 0.250

Asia WGS AF: 0.424 AC: 1471 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.6
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7836535; hg19: chr8-96705572;