dbSNP rs1155699: ENSG00000285899:n.227-3814G>A (chrX-43391471-G-A) – ACMG Classification: Likely_benign (-4 pts)

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000649774.1(ENSG00000285899):n.227-3814G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.60 ( 14153 hom., 19192 hem., cov: 22)

Failed GnomAD Quality Control

Consequence

ENSG00000285899
ENST00000649774.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.253

Publications

3 publications found

Variant links:

Genes affected

ENSG00000285899 (HGNC:):

ENSG00000285899 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -4 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.99).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000285899	ENST00000649774.1 link	n.227-3814G>A	intron_variant	Intron 3 of 7
ENSG00000285899	ENST00000811237.1 link	n.298-46864G>A	intron_variant	Intron 3 of 3
ENSG00000285899	ENST00000811238.1 link	n.253-3814G>A	intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes

AF:

0.596

AC:

65719

AN:

110176

Hom.:

14155

Cov.:

show subpopulations

Gnomad AFR

AF:

0.498

Gnomad AMI

AF:

0.539

Gnomad AMR

AF:

0.702

Gnomad ASJ

AF:

0.556

Gnomad EAS

AF:

0.594

Gnomad SAS

AF:

0.453

Gnomad FIN

AF:

0.615

Gnomad MID

AF:

0.647

Gnomad NFE

AF:

0.640

Gnomad OTH

AF:

0.600

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

GnomAD4 genome

Data not reliable, filtered out with message: InbreedingCoeff

AF:

0.597

AC:

65755

AN:

110228

Hom.:

14153

Cov.:

AF XY:

0.590

AC XY:

19192

AN XY:

32534

show subpopulations

African (AFR)

AF:

0.498

AC:

15095

AN:

30321

American (AMR)

AF:

0.702

AC:

7281

AN:

10365

Ashkenazi Jewish (ASJ)

AF:

0.556

AC:

1463

AN:

2629

East Asian (EAS)

AF:

0.595

AC:

2067

AN:

3476

South Asian (SAS)

AF:

0.455

AC:

1185

AN:

2606

European-Finnish (FIN)

AF:

0.615

AC:

3548

AN:

5771

Middle Eastern (MID)

AF:

0.629

AC:

132

AN:

210

European-Non Finnish (NFE)

AF:

0.640

AC:

33715

AN:

52665

Other (OTH)

AF:

0.600

AC:

906

AN:

1511

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

939

1878

2817

3756

4695

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

598

1196

1794

2392

2990

<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:

0.625

Hom.:

7540

Bravo

AF:

0.601

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.99

CADD

Benign

0.89

(source)

DANN

Benign

0.43

PhyloP100

0.25

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