8-95582541-T-C

Variant names:

• chr8-95582541-T-C
• rs2873824
• ENST00000517437.2:n.234-28123T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000517437.2(CFAP418-AS1):​n.234-28123T>C variant causes a intron 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 ENST00000517437.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.895
• Publications: 3 publications found

Genes affected

CFAP418-AS1 (HGNC:50444): (CFAP418 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
CFAP418-AS1	NR_038201.1	n.282-28123T>C		intron_variant	Intron 3 of 5
CFAP418-AS1	NR_038202.1	n.211-28123T>C		intron_variant	Intron 2 of 4
CFAP418-AS1	NR_038203.1	n.127-28123T>C		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CFAP418-AS1	ENST00000517437.2	n.234-28123T>C		intron_variant	Intron 2 of 4	3
CFAP418-AS1	ENST00000521905.3	n.305-28123T>C		intron_variant	Intron 3 of 4	5
CFAP418-AS1	ENST00000655917.1	n.297-28123T>C		intron_variant	Intron 3 of 4

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

African (AFR) AF: 0.747 AC: 30993 AN: 41472

American (AMR) AF: 0.765 AC: 11685 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.868 AC: 3014 AN: 3472

East Asian (EAS) AF: 0.685 AC: 3522 AN: 5144

South Asian (SAS) AF: 0.766 AC: 3691 AN: 4818

European-Finnish (FIN) AF: 0.793 AC: 8367 AN: 10546

Middle Eastern (MID) AF: 0.867 AC: 255 AN: 294

European-Non Finnish (NFE) AF: 0.813 AC: 55291 AN: 68002

Other (OTH) AF: 0.792 AC: 1676 AN: 2116

Alfa AF: 0.805 Hom.: 194067

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
PhyloP100		-0.90

Splicing

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

Other links and lift over

dbSNP: rs2873824; hg19: chr8-96594769;