Genetic Variant CXXC4-AS1:n.97-25696G>T (chr4-104617315-G-T) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BP4_StrongBS2

The ENST00000500179.1(CXXC4-AS1):n.97-25696G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00474 in 148,126 control chromosomes in the GnomAD database, including 3 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 0.0047 ( 3 hom., cov: 30)

Consequence

CXXC4-AS1
ENST00000500179.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.261

Publications

1 publications found

Variant links:

Genes affected

CXXC4-AS1 (HGNC:41054): (CXXC4 antisense RNA 1)

CXXC4-AS1 links:

ENSG00000248242 (HGNC:):

ENSG00000248242 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -8 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.98).

BS2

High Homozygotes in GnomAd4 at 3 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CXXC4-AS1	NR_125926.1 link	n.97-25696G>T		intron_variant	Intron 1 of 9
LOC124900745	XR_007058211.1 link	n.2113+36512C>A		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
CXXC4-AS1	ENST00000500179.1 link	n.97-25696G>T	intron_variant	Intron 1 of 9	2
CXXC4-AS1	ENST00000664466.1 link	n.213-20583G>T	intron_variant	Intron 1 of 4
ENSG00000248242	ENST00000723032.1 link	n.428+36512C>A	intron_variant	Intron 3 of 5

Frequencies

GnomAD3 genomes

AF:

0.00473

AC:

700

AN:

148034

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00131

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00216

Gnomad ASJ

AF:

0.00347

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00847

Gnomad FIN

AF:

0.00461

Gnomad MID

AF:

0.0130

Gnomad NFE

AF:

0.00743

Gnomad OTH

AF:

0.00744

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

GnomAD4 genome

AF:

0.00474

AC:

702

AN:

148126

Hom.:

Cov.:

AF XY:

0.00485

AC XY:

349

AN XY:

71994

show subpopulations

African (AFR)

AF:

0.00131

AC:

AN:

39816

American (AMR)

AF:

0.00215

AC:

AN:

14858

Ashkenazi Jewish (ASJ)

AF:

0.00347

AC:

AN:

3456

East Asian (EAS)

AF:

0.00

AC:

AN:

5060

South Asian (SAS)

AF:

0.00893

AC:

AN:

4702

European-Finnish (FIN)

AF:

0.00461

AC:

AN:

9540

Middle Eastern (MID)

AF:

0.0141

AC:

AN:

284

European-Non Finnish (NFE)

AF:

0.00743

AC:

501

AN:

67462

Other (OTH)

AF:

0.00735

AC:

AN:

2040

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

131

164

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

100

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.00179

Hom.:

263

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.98

CADD

Benign

0.72

(source)

DANN

Benign

0.51

PhyloP100

-0.26

Mutation Taster

=100/0

polymorphism

(source)

Splicing

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

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over