dbSNP rs3104964: CFAP418-AS1:n.145-27156G>A (chr8-95583508-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000517437.1(CFAP418-AS1):n.145-27156G>A variant causes a intron 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
ENST00000517437.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.622

Variant links:

Genes affected

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

CFAP418-AS1 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=-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	Effect	Exon rank
CFAP418-AS1	NR_038201.1 link	n.282-27156G>A	intron_variant	Intron 3 of 5
CFAP418-AS1	NR_038202.1 link	n.211-27156G>A	intron_variant	Intron 2 of 4
CFAP418-AS1	NR_038203.1 link	n.127-27156G>A	intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
CFAP418-AS1	ENST00000517437.1 link	n.145-27156G>A	intron_variant	Intron 1 of 3	3
CFAP418-AS1	ENST00000521905.2 link	n.288-27156G>A	intron_variant	Intron 3 of 4	5
CFAP418-AS1	ENST00000655917.1 link	n.297-27156G>A	intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes

AF:

0.568

AC:

86234

AN:

151888

Hom.:

24640

Cov.:

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.:

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.

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