dbSNP rs6526342: SAT1-DT:n.231+947T>G (chrX-23781621-A-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 ENST00000366134.3(SAT1-DT):n.231+947T>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 0.67 ( 18175 hom., 20758 hem., cov: 21)

Failed GnomAD Quality Control

Consequence

SAT1-DT
ENST00000366134.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.65

Publications

12 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=-0.68).

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
SAT1-DT	NR_184056.1 link	n.419+947T>G	intron_variant	Intron 1 of 4
SAT1-DT	NR_184057.1 link	n.102+1264T>G	intron_variant	Intron 1 of 4
SAT1-DT	NR_184058.1 link	n.419+947T>G	intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
SAT1-DT	ENST00000366134.3 link	n.231+947T>G	intron_variant	Intron 2 of 2	3
SAT1-DT	ENST00000737050.1 link	n.839+947T>G	intron_variant	Intron 1 of 1
SAT1-DT	ENST00000737051.1 link	n.190+1264T>G	intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.671

AC:

72696

AN:

108348

Hom.:

18172

Cov.:

show subpopulations

Gnomad AFR

AF:

0.468

Gnomad AMI

AF:

0.806

Gnomad AMR

AF:

0.572

Gnomad ASJ

AF:

0.748

Gnomad EAS

AF:

0.609

Gnomad SAS

AF:

0.827

Gnomad FIN

AF:

0.770

Gnomad MID

AF:

0.625

Gnomad NFE

AF:

0.786

Gnomad OTH

AF:

0.664

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:

0.671

AC:

72731

AN:

108397

Hom.:

18175

Cov.:

AF XY:

0.674

AC XY:

20758

AN XY:

30813

show subpopulations

African (AFR)

AF:

0.469

AC:

13961

AN:

29791

American (AMR)

AF:

0.571

AC:

5659

AN:

9910

Ashkenazi Jewish (ASJ)

AF:

0.748

AC:

1957

AN:

2615

East Asian (EAS)

AF:

0.610

AC:

2077

AN:

3407

South Asian (SAS)

AF:

0.826

AC:

2111

AN:

2556

European-Finnish (FIN)

AF:

0.770

AC:

4070

AN:

5285

Middle Eastern (MID)

AF:

0.635

AC:

134

AN:

211

European-Non Finnish (NFE)

AF:

0.786

AC:

41242

AN:

52488

Other (OTH)

AF:

0.669

AC:

979

AN:

1463

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.513

Heterozygous variant carriers

798

1595

2393

3190

3988

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

656

1312

1968

2624

3280

<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:

0.701

Hom.:

19368

Bravo

AF:

0.642

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.68

CADD

Benign

(source)

DANN

Benign

0.84

PhyloP100

1.7

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