rs1500899

Variant names:

• chr8-95522762-G-T
• rs1500899
• ENST00000517437.2:n.234-87902G>T

Variant summary

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

The ENST00000517437.2(CFAP418-AS1):​n.234-87902G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.304 in 152,070 control chromosomes in the GnomAD database, including 7,182 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 0.30 (7182 hom., cov: 32)
• Consequence: CFAP418-AS1 ENST00000517437.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.922
• Publications: 5 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=-1.04).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.35 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000517437.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CFAP418-AS1	NR_038201.1		n.282-87902G>T		intron	N/A
	CFAP418-AS1	NR_038202.1		n.211-87902G>T		intron	N/A
	CFAP418-AS1	NR_038203.1		n.127-87902G>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CFAP418-AS1	ENST00000517437.2	TSL:3	n.234-87902G>T		intron	N/A
	CFAP418-AS1	ENST00000519366.1	TSL:5	n.269-1645G>T		intron	N/A
	CFAP418-AS1	ENST00000521905.3	TSL:5	n.305-87902G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.304 AC: 46197 AN: 151950 Hom.: 7163 Cov.: 32

Gnomad AFR AF: 0.265

Gnomad AMI AF: 0.281

Gnomad AMR AF: 0.333

Gnomad ASJ AF: 0.374

Gnomad EAS AF: 0.362

Gnomad SAS AF: 0.254

Gnomad FIN AF: 0.287

Gnomad MID AF: 0.293

Gnomad NFE AF: 0.320

Gnomad OTH AF: 0.318

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

GnomAD4 genome AF: 0.304 AC: 46258 AN: 152070 Hom.: 7182 Cov.: 32 AF XY: 0.305 AC XY: 22664 AN XY: 74326

African (AFR) AF: 0.265 AC: 10990 AN: 41462

American (AMR) AF: 0.333 AC: 5098 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.374 AC: 1294 AN: 3460

East Asian (EAS) AF: 0.364 AC: 1880 AN: 5168

South Asian (SAS) AF: 0.254 AC: 1221 AN: 4808

European-Finnish (FIN) AF: 0.287 AC: 3037 AN: 10576

Middle Eastern (MID) AF: 0.279 AC: 82 AN: 294

European-Non Finnish (NFE) AF: 0.320 AC: 21731 AN: 67988

Other (OTH) AF: 0.316 AC: 669 AN: 2114

Alfa AF: 0.316 Hom.: 7050

Bravo AF: 0.311

Asia WGS AF: 0.330 AC: 1148 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.21
DANN	Benign	0.59
PhyloP100		-0.92

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1500899;

hg19: chr8-96534990;