dbSNP rs763299: ENSG00000286072:n.277+24412T>C (chrX-112871491-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 ENST00000738665.1(ENSG00000286072):n.277+24412T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.105 in 111,221 control chromosomes in the GnomAD database, including 1,138 homozygotes. There are 3,184 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 0.10 ( 1138 hom., 3184 hem., cov: 22)

Consequence

ENSG00000286072
ENST00000738665.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.376

Publications

1 publications found

Variant links:

Genes affected

ENSG00000286072 (HGNC:):

ENSG00000286072 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=-0.86).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.283 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000286072	ENST00000738665.1 link	n.277+24412T>C	intron_variant	Intron 2 of 2
ENSG00000286072	ENST00000738666.1 link	n.396+24412T>C	intron_variant	Intron 3 of 3
ENSG00000286072	ENST00000738667.1 link	n.410+24412T>C	intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes

AF:

0.104

AC:

11617

AN:

111173

Hom.:

1138

Cov.:

show subpopulations

Gnomad AFR

AF:

0.288

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.153

Gnomad ASJ

AF:

0.0136

Gnomad EAS

AF:

0.190

Gnomad SAS

AF:

0.0713

Gnomad FIN

AF:

0.00116

Gnomad MID

AF:

0.0460

Gnomad NFE

AF:

0.00427

Gnomad OTH

AF:

0.101

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

GnomAD4 genome

AF:

0.105

AC:

11645

AN:

111221

Hom.:

1138

Cov.:

AF XY:

0.0952

AC XY:

3184

AN XY:

33443

show subpopulations

African (AFR)

AF:

0.288

AC:

8746

AN:

30404

American (AMR)

AF:

0.154

AC:

1608

AN:

10455

Ashkenazi Jewish (ASJ)

AF:

0.0136

AC:

AN:

2639

East Asian (EAS)

AF:

0.190

AC:

668

AN:

3509

South Asian (SAS)

AF:

0.0712

AC:

188

AN:

2639

European-Finnish (FIN)

AF:

0.00116

AC:

AN:

6029

Middle Eastern (MID)

AF:

0.0461

AC:

AN:

217

European-Non Finnish (NFE)

AF:

0.00427

AC:

227

AN:

53119

Other (OTH)

AF:

0.102

AC:

155

AN:

1524

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

314

629

943

1258

1572

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

116

232

348

464

580

<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:

0.0595

Hom.:

299

Bravo

AF:

0.126

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

6.9

(source)

DANN

Benign

0.69

PhyloP100

0.38

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