rs6982567

Positions:

• chr8-95738053-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.179-62443C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.237 in 152,036 control chromosomes in the GnomAD database, including 4,650 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 (4650 hom., cov: 32)
• Consequence: CFAP418-AS1 ENST00000517437.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.18

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 (AFR) allele frequency at 95% confidence interval = 0.328 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CFAP418-AS1	NR_038201.1	n.316-62443C>T		intron_variant
CFAP418-AS1	NR_038202.1	n.245-62443C>T		intron_variant
CFAP418-AS1	NR_038203.1	n.161-62443C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CFAP418-AS1	ENST00000517437.1	n.179-62443C>T		intron_variant		3
CFAP418-AS1	ENST00000655917.1	n.331-62443C>T		intron_variant
CFAP418-AS1	ENST00000664790.1	n.35-62443C>T		intron_variant
CFAP418-AS1	ENST00000671532.1	n.258-62443C>T		intron_variant

Frequencies

GnomAD3 genomes AF: 0.237 AC: 35957 AN: 151918 Hom.: 4637 Cov.: 32

Gnomad AFR AF: 0.332

Gnomad AMI AF: 0.172

Gnomad AMR AF: 0.245

Gnomad ASJ AF: 0.196

Gnomad EAS AF: 0.266

Gnomad SAS AF: 0.204

Gnomad FIN AF: 0.188

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.187

Gnomad OTH AF: 0.245

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

GnomAD4 genome AF: 0.237 AC: 36007 AN: 152036 Hom.: 4650 Cov.: 32 AF XY: 0.237 AC XY: 17606 AN XY: 74274

Gnomad4 AFR AF: 0.332

Gnomad4 AMR AF: 0.245

Gnomad4 ASJ AF: 0.196

Gnomad4 EAS AF: 0.265

Gnomad4 SAS AF: 0.204

Gnomad4 FIN AF: 0.188

Gnomad4 NFE AF: 0.187

Gnomad4 OTH AF: 0.249

Alfa AF: 0.199 Hom.: 4048

Bravo AF: 0.247

Asia WGS AF: 0.236 AC: 822 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	0.077
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6982567; hg19: chr8-96750281;