Genetic Variant ENST00000821191.1:n.463+31852T>G (chrX-148161331-T-G) – 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 ENST00000821191.1(ENSG00000306798):n.463+31852T>G 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 0.74 ( 21715 hom., 23462 hem., cov: 22)

Failed GnomAD Quality Control

Consequence

ENSG00000306798
ENST00000821191.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.323

Publications

5 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: Likely_benign. The variant received -4 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.81).

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.463+31852T>G		intron_variant	Intron 1 of 2
ENSG00000306798	ENST00000821192.1 link	n.221+31852T>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.743

AC:

81311

AN:

109457

Hom.:

21708

Cov.:

show subpopulations

Gnomad AFR

AF:

0.794

Gnomad AMI

AF:

0.834

Gnomad AMR

AF:

0.774

Gnomad ASJ

AF:

0.591

Gnomad EAS

AF:

0.827

Gnomad SAS

AF:

0.628

Gnomad FIN

AF:

0.680

Gnomad MID

AF:

0.697

Gnomad NFE

AF:

0.721

Gnomad OTH

AF:

0.736

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:

0.743

AC:

81349

AN:

109507

Hom.:

21715

Cov.:

AF XY:

0.738

AC XY:

23462

AN XY:

31805

show subpopulations

African (AFR)

AF:

0.793

AC:

23887

AN:

30105

American (AMR)

AF:

0.774

AC:

7910

AN:

10214

Ashkenazi Jewish (ASJ)

AF:

0.591

AC:

1542

AN:

2610

East Asian (EAS)

AF:

0.828

AC:

2835

AN:

3423

South Asian (SAS)

AF:

0.626

AC:

1578

AN:

2519

European-Finnish (FIN)

AF:

0.680

AC:

3876

AN:

5704

Middle Eastern (MID)

AF:

0.700

AC:

152

AN:

217

European-Non Finnish (NFE)

AF:

0.721

AC:

37897

AN:

52538

Other (OTH)

AF:

0.738

AC:

1105

AN:

1497

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

726

1451

2177

2902

3628

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

686

1372

2058

2744

3430

<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:

0.736

Hom.:

82445

Bravo

AF:

0.762

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

5.9

(source)

DANN

Benign

0.56

PhyloP100

0.32

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