chr8-95226180-T-C

Position:

• chr8-95226180-T-C

Variant summary

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

The ENST00000517655.1(CFAP418-AS1):​n.521+20868T>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 0.394 in 152,164 control chromosomes in the GnomAD database, including 12,618 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 0.39 (12618 hom., cov: 32)
• Consequence: CFAP418-AS1 ENST00000517655.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.99

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=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.498 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CFAP418-AS1	ENST00000517655.1	n.521+20868T>C		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.394 AC: 59961 AN: 152044 Hom.: 12600 Cov.: 32

Gnomad AFR AF: 0.271

Gnomad AMI AF: 0.570

Gnomad AMR AF: 0.347

Gnomad ASJ AF: 0.453

Gnomad EAS AF: 0.200

Gnomad SAS AF: 0.514

Gnomad FIN AF: 0.430

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.475

Gnomad OTH AF: 0.402

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

GnomAD4 genome AF: 0.394 AC: 60016 AN: 152164 Hom.: 12618 Cov.: 32 AF XY: 0.392 AC XY: 29190 AN XY: 74386

Gnomad4 AFR AF: 0.271

Gnomad4 AMR AF: 0.347

Gnomad4 ASJ AF: 0.453

Gnomad4 EAS AF: 0.200

Gnomad4 SAS AF: 0.515

Gnomad4 FIN AF: 0.430

Gnomad4 NFE AF: 0.475

Gnomad4 OTH AF: 0.409

Alfa AF: 0.452 Hom.: 15496

Bravo AF: 0.378

Asia WGS AF: 0.354 AC: 1234 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.013
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: rs894151; hg19: chr8-96238408;