Variant rs1500899 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000517437.1(CFAP418-AS1):n.145-87902G>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
ENST00000517437.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.922

Variant links:

Genes affected

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

CFAP418-AS1 links:

ENSG00000253872 (HGNC:):

ENSG00000253872 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect
CFAP418-AS1	NR_038201.1 link	n.282-87902G>T	intron_variant
CFAP418-AS1	NR_038202.1 link	n.211-87902G>T	intron_variant
CFAP418-AS1	NR_038203.1 link	n.127-87902G>T	intron_variant

Ensembl

Gene	Transcript	HGVSc	Effect	TSL
CFAP418-AS1	ENST00000517437.1 link	n.145-87902G>T	intron_variant	3
ENSG00000253872	ENST00000519366.1 link	n.269-1645G>T	intron_variant	5
CFAP418-AS1	ENST00000521905.2 link	n.288-87902G>T	intron_variant	5

Frequencies

GnomAD3 genomes

AF:

0.304

AC:

46197

AN:

151950

Hom.:

7163

Cov.:

show subpopulations

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.:

AF XY:

0.305

AC XY:

22664

AN XY:

74326

show subpopulations

Gnomad4 AFR

AF:

0.265

Gnomad4 AMR

AF:

0.333

Gnomad4 ASJ

AF:

0.374

Gnomad4 EAS

AF:

0.364

Gnomad4 SAS

AF:

0.254

Gnomad4 FIN

AF:

0.287

Gnomad4 NFE

AF:

0.320

Gnomad4 OTH

AF:

0.316

Alfa

AF:

0.315

Hom.:

6011

Bravo

AF:

0.311

Asia WGS

AF:

0.330

AC:

1148

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

0.21

DANN

Benign

0.59

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over