Genetic Variant SAT1-DT:n.231+752G>A (chrX-23781816-C-T) – 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 ENST00000366134.3(SAT1-DT):n.231+752G>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 0.65 ( 16341 hom., 10129 hem., cov: 13)

Failed GnomAD Quality Control

Consequence

SAT1-DT
ENST00000366134.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.929

Publications

5 publications found

Variant links:

Genes affected

SAT1-DT (HGNC:56726): (SAT1 divergent transcript)

SAT1-DT 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	Effect	Exon rank
SAT1-DT	NR_184056.1 link	n.419+752G>A	intron_variant	Intron 1 of 4
SAT1-DT	NR_184057.1 link	n.102+1069G>A	intron_variant	Intron 1 of 4
SAT1-DT	NR_184058.1 link	n.419+752G>A	intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
SAT1-DT	ENST00000366134.3 link	n.231+752G>A	intron_variant	Intron 2 of 2	3
SAT1-DT	ENST00000737050.1 link	n.839+752G>A	intron_variant	Intron 1 of 1
SAT1-DT	ENST00000737051.1 link	n.190+1069G>A	intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.654

AC:

56867

AN:

87000

Hom.:

16335

Cov.:

show subpopulations

Gnomad AFR

AF:

0.368

Gnomad AMI

AF:

0.799

Gnomad AMR

AF:

0.588

Gnomad ASJ

AF:

0.736

Gnomad EAS

AF:

0.612

Gnomad SAS

AF:

0.831

Gnomad FIN

AF:

0.775

Gnomad MID

AF:

0.661

Gnomad NFE

AF:

0.784

Gnomad OTH

AF:

0.654

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:

0.654

AC:

56888

AN:

87016

Hom.:

16341

Cov.:

AF XY:

0.639

AC XY:

10129

AN XY:

15852

show subpopulations

African (AFR)

AF:

0.369

AC:

8293

AN:

22481

American (AMR)

AF:

0.587

AC:

4028

AN:

6862

Ashkenazi Jewish (ASJ)

AF:

0.736

AC:

1756

AN:

2385

East Asian (EAS)

AF:

0.613

AC:

1649

AN:

2691

South Asian (SAS)

AF:

0.830

AC:

1291

AN:

1555

European-Finnish (FIN)

AF:

0.775

AC:

2071

AN:

2673

Middle Eastern (MID)

AF:

0.675

AC:

104

AN:

154

European-Non Finnish (NFE)

AF:

0.784

AC:

36517

AN:

46550

Other (OTH)

AF:

0.661

AC:

722

AN:

1093

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.519

Heterozygous variant carriers

629

1258

1886

2515

3144

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

464

928

1392

1856

2320

<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:

0.469

Hom.:

1514

Bravo

AF:

0.603

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

2.1

(source)

DANN

Benign

0.94

PhyloP100

-0.93

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