dbSNP rs4129664: ENSG00000294456:n.470+73275T>C (chrX-25551046-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000723704.1(ENSG00000294456):n.470+73275T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.12 in 111,592 control chromosomes in the GnomAD database, including 1,810 homozygotes. There are 3,588 hemizygotes in GnomAD. 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 0.12 ( 1810 hom., 3588 hem., cov: 22)

Consequence

ENSG00000294456
ENST00000723704.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0800

Publications

0 publications found

Variant links:

Genes affected

ENSG00000294456 (HGNC:):

ENSG00000294456 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.91).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.391 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000294456	ENST00000723704.1 link	n.470+73275T>C	intron_variant	Intron 5 of 5
ENSG00000294456	ENST00000723705.1 link	n.521+73275T>C	intron_variant	Intron 6 of 6
ENSG00000294456	ENST00000723707.1 link	n.396+73275T>C	intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes

AF:

0.120

AC:

13339

AN:

111541

Hom.:

1811

Cov.:

show subpopulations

Gnomad AFR

AF:

0.397

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0480

Gnomad ASJ

AF:

0.0324

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00745

Gnomad FIN

AF:

0.00211

Gnomad MID

AF:

0.0546

Gnomad NFE

AF:

0.00907

Gnomad OTH

AF:

0.0965

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

GnomAD4 genome

AF:

0.120

AC:

13355

AN:

111592

Hom.:

1810

Cov.:

AF XY:

0.106

AC XY:

3588

AN XY:

33834

show subpopulations

African (AFR)

AF:

0.397

AC:

12095

AN:

30443

American (AMR)

AF:

0.0477

AC:

504

AN:

10565

Ashkenazi Jewish (ASJ)

AF:

0.0324

AC:

AN:

2653

East Asian (EAS)

AF:

0.00

AC:

AN:

3524

South Asian (SAS)

AF:

0.00710

AC:

AN:

2676

European-Finnish (FIN)

AF:

0.00211

AC:

AN:

6160

Middle Eastern (MID)

AF:

0.0507

AC:

AN:

217

European-Non Finnish (NFE)

AF:

0.00907

AC:

482

AN:

53145

Other (OTH)

AF:

0.0953

AC:

145

AN:

1521

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

311

623

934

1246

1557

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

124

248

372

496

620

<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:

0.0614

Hom.:

1797

Bravo

AF:

0.140

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

3.4

(source)

DANN

Benign

0.63

PhyloP100

0.080

Splicing

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

Publications

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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