rs3104964

Variant summary

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

The NR_038201.1(CFAP418-AS1):​n.282-27156G>A 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 0.568 in 152,004 control chromosomes in the GnomAD database, including 24,651 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 0.57 ( 24651 hom., cov: 33)

Consequence

CFAP418-AS1
NR_038201.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.622
Variant links:
Genes affected
CFAP418-AS1 (HGNC:50444): (CFAP418 antisense RNA 1)

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=-0.95).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.601 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
CFAP418-AS1NR_038201.1 linkuse as main transcriptn.282-27156G>A intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CFAP418-AS1ENST00000655917.1 linkuse as main transcriptn.297-27156G>A intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
AF:
0.568
AC:
86234
AN:
151888
Hom.:
24640
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.493
Gnomad AMI
AF:
0.651
Gnomad AMR
AF:
0.573
Gnomad ASJ
AF:
0.554
Gnomad EAS
AF:
0.521
Gnomad SAS
AF:
0.621
Gnomad FIN
AF:
0.635
Gnomad MID
AF:
0.525
Gnomad NFE
AF:
0.601
Gnomad OTH
AF:
0.562
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.568
AC:
86279
AN:
152004
Hom.:
24651
Cov.:
33
AF XY:
0.570
AC XY:
42325
AN XY:
74294
show subpopulations
Gnomad4 AFR
AF:
0.494
Gnomad4 AMR
AF:
0.573
Gnomad4 ASJ
AF:
0.554
Gnomad4 EAS
AF:
0.522
Gnomad4 SAS
AF:
0.619
Gnomad4 FIN
AF:
0.635
Gnomad4 NFE
AF:
0.601
Gnomad4 OTH
AF:
0.559
Alfa
AF:
0.554
Hom.:
5844
Bravo
AF:
0.558
Asia WGS
AF:
0.595
AC:
2069
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.95
CADD
Benign
3.2
DANN
Benign
0.18

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.

Other links and lift over

dbSNP: rs3104964; hg19: chr8-96595736; API