chr8-95582541-T-C

Position:

• chr8-95582541-T-C

Variant summary

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

The NR_038201.1(CFAP418-AS1):​n.282-28123T>C 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 0.784 in 152,048 control chromosomes in the GnomAD database, including 46,935 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 0.78 (46935 hom., cov: 31)
• Consequence: CFAP418-AS1 NR_038201.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.895

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=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.807 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CFAP418-AS1	NR_038201.1	n.282-28123T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CFAP418-AS1	ENST00000655917.1	n.297-28123T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.784 AC: 119172 AN: 151930 Hom.: 46910 Cov.: 31

Gnomad AFR AF: 0.747

Gnomad AMI AF: 0.830

Gnomad AMR AF: 0.765

Gnomad ASJ AF: 0.868

Gnomad EAS AF: 0.685

Gnomad SAS AF: 0.766

Gnomad FIN AF: 0.793

Gnomad MID AF: 0.861

Gnomad NFE AF: 0.813

Gnomad OTH AF: 0.791

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

GnomAD4 genome AF: 0.784 AC: 119251 AN: 152048 Hom.: 46935 Cov.: 31 AF XY: 0.784 AC XY: 58233 AN XY: 74310

Gnomad4 AFR AF: 0.747

Gnomad4 AMR AF: 0.765

Gnomad4 ASJ AF: 0.868

Gnomad4 EAS AF: 0.685

Gnomad4 SAS AF: 0.766

Gnomad4 FIN AF: 0.793

Gnomad4 NFE AF: 0.813

Gnomad4 OTH AF: 0.792

Alfa AF: 0.809 Hom.: 95662

Bravo AF: 0.781

Asia WGS AF: 0.700 AC: 2436 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.4
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2873824; hg19: chr8-96594769;