chr8-95752030-T-G

Position:

• chr8-95752030-T-G

Variant summary

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

The NR_038201.1(CFAP418-AS1):​n.316-48466T>G 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 0.815 in 152,178 control chromosomes in the GnomAD database, including 50,667 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 0.81 (50667 hom., cov: 33)
• Consequence: CFAP418-AS1 NR_038201.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.729

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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.874 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CFAP418-AS1	NR_038201.1	n.316-48466T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CFAP418-AS1	ENST00000655917.1	n.331-48466T>G		intron_variant, non_coding_transcript_variant
CFAP418-AS1	ENST00000517437.1	n.179-48466T>G		intron_variant, non_coding_transcript_variant		3
CFAP418-AS1	ENST00000664790.1	n.35-48466T>G		intron_variant, non_coding_transcript_variant
CFAP418-AS1	ENST00000671532.1	n.258-48466T>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.814 AC: 123847 AN: 152058 Hom.: 50608 Cov.: 33

Gnomad AFR AF: 0.881

Gnomad AMI AF: 0.679

Gnomad AMR AF: 0.821

Gnomad ASJ AF: 0.683

Gnomad EAS AF: 0.847

Gnomad SAS AF: 0.818

Gnomad FIN AF: 0.809

Gnomad MID AF: 0.772

Gnomad NFE AF: 0.779

Gnomad OTH AF: 0.807

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

GnomAD4 genome AF: 0.815 AC: 123969 AN: 152178 Hom.: 50667 Cov.: 33 AF XY: 0.817 AC XY: 60789 AN XY: 74380

Gnomad4 AFR AF: 0.881

Gnomad4 AMR AF: 0.821

Gnomad4 ASJ AF: 0.683

Gnomad4 EAS AF: 0.847

Gnomad4 SAS AF: 0.819

Gnomad4 FIN AF: 0.809

Gnomad4 NFE AF: 0.779

Gnomad4 OTH AF: 0.810

Alfa AF: 0.786 Hom.: 61798

Bravo AF: 0.819

Asia WGS AF: 0.836 AC: 2907 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	7.0
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7817825; hg19: chr8-96764258;