dbSNP rs993010: ENSG00000233928:n.287-2904T>C (chrX-34073562-T-C) – 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 ENST00000653446.1(ENSG00000233928):n.287-2904T>C 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 0.56 ( 12865 hom., 17902 hem., cov: 22)

Failed GnomAD Quality Control

Consequence

ENSG00000233928
ENST00000653446.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.113

Publications

2 publications found

Variant links:

Genes affected

ENSG00000233928 (HGNC:):

ENSG00000233928 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=-0.9).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105373153	XR_950542.4 link	n.372-2904T>C		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000233928	ENST00000653446.1 link	n.287-2904T>C	intron_variant	Intron 2 of 5
ENSG00000233928	ENST00000656777.1 link	n.349-2904T>C	intron_variant	Intron 2 of 4
ENSG00000233928	ENST00000656973.1 link	n.201-2904T>C	intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes

AF:

0.560

AC:

61633

AN:

110141

Hom.:

12871

Cov.:

show subpopulations

Gnomad AFR

AF:

0.425

Gnomad AMI

AF:

0.513

Gnomad AMR

AF:

0.503

Gnomad ASJ

AF:

0.569

Gnomad EAS

AF:

0.269

Gnomad SAS

AF:

0.416

Gnomad FIN

AF:

0.628

Gnomad MID

AF:

0.645

Gnomad NFE

AF:

0.666

Gnomad OTH

AF:

0.571

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:

0.559

AC:

61631

AN:

110194

Hom.:

12865

Cov.:

AF XY:

0.550

AC XY:

17902

AN XY:

32532

show subpopulations

African (AFR)

AF:

0.425

AC:

12866

AN:

30298

American (AMR)

AF:

0.502

AC:

5176

AN:

10307

Ashkenazi Jewish (ASJ)

AF:

0.569

AC:

1497

AN:

2633

East Asian (EAS)

AF:

0.270

AC:

937

AN:

3469

South Asian (SAS)

AF:

0.416

AC:

1098

AN:

2638

European-Finnish (FIN)

AF:

0.628

AC:

3660

AN:

5825

Middle Eastern (MID)

AF:

0.653

AC:

139

AN:

213

European-Non Finnish (NFE)

AF:

0.666

AC:

35061

AN:

52643

Other (OTH)

AF:

0.570

AC:

852

AN:

1496

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

950

1900

2850

3800

4750

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

570

1140

1710

2280

2850

<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:

0.615

Hom.:

88290

Bravo

AF:

0.542

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

6.8

(source)

DANN

Benign

0.66

PhyloP100

0.11

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