dbSNP rs5936441: ENSG00000306798:n.688-12416C>T (chrX-148242736-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000821191.1(ENSG00000306798):n.688-12416C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.451 in 108,844 control chromosomes in the GnomAD database, including 9,588 homozygotes. There are 13,381 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 0.45 ( 9588 hom., 13381 hem., cov: 21)

Consequence

ENSG00000306798
ENST00000821191.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.832

Publications

3 publications found

Variant links:

Genes affected

ENSG00000306798 (HGNC:):

ENSG00000306798 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=-1.03).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.728 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000306798	ENST00000821191.1 link	n.688-12416C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.451

AC:

49065

AN:

108794

Hom.:

9585

Cov.:

show subpopulations

Gnomad AFR

AF:

0.736

Gnomad AMI

AF:

0.162

Gnomad AMR

AF:

0.265

Gnomad ASJ

AF:

0.475

Gnomad EAS

AF:

0.185

Gnomad SAS

AF:

0.426

Gnomad FIN

AF:

0.332

Gnomad MID

AF:

0.421

Gnomad NFE

AF:

0.361

Gnomad OTH

AF:

0.409

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

GnomAD4 genome

AF:

0.451

AC:

49104

AN:

108844

Hom.:

9588

Cov.:

AF XY:

0.428

AC XY:

13381

AN XY:

31248

show subpopulations

African (AFR)

AF:

0.736

AC:

21915

AN:

29776

American (AMR)

AF:

0.265

AC:

2714

AN:

10246

Ashkenazi Jewish (ASJ)

AF:

0.475

AC:

1238

AN:

2609

East Asian (EAS)

AF:

0.184

AC:

635

AN:

3447

South Asian (SAS)

AF:

0.426

AC:

1065

AN:

2501

European-Finnish (FIN)

AF:

0.332

AC:

1831

AN:

5508

Middle Eastern (MID)

AF:

0.444

AC:

AN:

214

European-Non Finnish (NFE)

AF:

0.361

AC:

18895

AN:

52388

Other (OTH)

AF:

0.409

AC:

608

AN:

1487

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

862

1724

2587

3449

4311

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

450

900

1350

1800

2250

<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:

0.390

Hom.:

33519

Bravo

AF:

0.454

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.34

(source)

DANN

Benign

0.73

PhyloP100

-0.83

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