rs2016718

Positions:

• chr8-95731977-G-A

Variant summary

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

The NR_038201.1(CFAP418-AS1):​n.316-68519G>A 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 0.625 in 152,112 control chromosomes in the GnomAD database, including 31,037 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 0.62 (31037 hom., cov: 32)
• Consequence: CFAP418-AS1 NR_038201.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.757

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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.844 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CFAP418-AS1	NR_038201.1	n.316-68519G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CFAP418-AS1	ENST00000655917.1	n.331-68519G>A		intron_variant, non_coding_transcript_variant
CFAP418-AS1	ENST00000517437.1	n.179-68519G>A		intron_variant, non_coding_transcript_variant		3
CFAP418-AS1	ENST00000664790.1	n.35-68519G>A		intron_variant, non_coding_transcript_variant
CFAP418-AS1	ENST00000671532.1	n.258-68519G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.625 AC: 94940 AN: 151994 Hom.: 30974 Cov.: 32

Gnomad AFR AF: 0.790

Gnomad AMI AF: 0.544

Gnomad AMR AF: 0.639

Gnomad ASJ AF: 0.697

Gnomad EAS AF: 0.866

Gnomad SAS AF: 0.739

Gnomad FIN AF: 0.485

Gnomad MID AF: 0.674

Gnomad NFE AF: 0.513

Gnomad OTH AF: 0.619

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

GnomAD4 genome AF: 0.625 AC: 95060 AN: 152112 Hom.: 31037 Cov.: 32 AF XY: 0.626 AC XY: 46556 AN XY: 74342

Gnomad4 AFR AF: 0.790

Gnomad4 AMR AF: 0.639

Gnomad4 ASJ AF: 0.697

Gnomad4 EAS AF: 0.866

Gnomad4 SAS AF: 0.738

Gnomad4 FIN AF: 0.485

Gnomad4 NFE AF: 0.513

Gnomad4 OTH AF: 0.623

Alfa AF: 0.608 Hom.: 4206

Bravo AF: 0.645

Asia WGS AF: 0.813 AC: 2829 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.083
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2016718; hg19: chr8-96744205;