dbSNP rs3764885: SAT1:c.66+59A>G (chrX-23783476-A-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 NM_002970.4(SAT1):c.66+59A>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 0.72 ( 20457 hom., 22856 hem., cov: 22)

Exomes 𝑓: 0.78 ( 210336 hom. 230774 hem. )

Failed GnomAD Quality Control

Consequence

SAT1
NM_002970.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.244

Publications

9 publications found

Variant links:

Genes affected

SAT1 (HGNC:10540): (spermidine/spermine N1-acetyltransferase 1) The protein encoded by this gene belongs to the acetyltransferase family, and is a rate-limiting enzyme in the catabolic pathway of polyamine metabolism. It catalyzes the acetylation of spermidine and spermine, and is involved in the regulation of the intracellular concentration of polyamines and their transport out of cells. Defects in this gene are associated with keratosis follicularis spinulosa decalvans (KFSD). Alternatively spliced transcripts have been found for this gene.[provided by RefSeq, Sep 2009]

SAT1 links:

LOC127933115 (HGNC:0):

LOC127933115 links:

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=-0.84).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002970.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
SAT1	NM_002970.4	MANE Select	c.66+59A>G	intron	N/A	NP_002961.1
SAT1	NR_027783.3		n.245+59A>G	intron	N/A
LOC127933115	NM_001414725.1	MANE Select	c.*109A>G	downstream_gene	N/A	NP_001401654.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
SAT1	ENST00000379270.5	TSL:1 MANE Select	c.66+59A>G	intron	N/A	ENSP00000368572.4
SAT1	ENST00000379254.5	TSL:3	c.66+59A>G	intron	N/A	ENSP00000368556.1
SAT1	ENST00000379251.7	TSL:2	n.245+59A>G	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.719

AC:

78839

AN:

109630

Hom.:

20451

Cov.:

show subpopulations

Gnomad AFR

AF:

0.626

Gnomad AMI

AF:

0.807

Gnomad AMR

AF:

0.591

Gnomad ASJ

AF:

0.762

Gnomad EAS

AF:

0.607

Gnomad SAS

AF:

0.822

Gnomad FIN

AF:

0.768

Gnomad MID

AF:

0.625

Gnomad NFE

AF:

0.792

Gnomad OTH

AF:

0.717

GnomAD4 exome

Data not reliable, filtered out with message: InbreedingCoeff

AF:

0.784

AC:

769920

AN:

981905

Hom.:

210336

Cov.:

AF XY:

0.806

AC XY:

230774

AN XY:

286151

show subpopulations

African (AFR)

AF:

0.623

AC:

15024

AN:

24123

American (AMR)

AF:

0.555

AC:

17675

AN:

31859

Ashkenazi Jewish (ASJ)

AF:

0.768

AC:

13591

AN:

17688

East Asian (EAS)

AF:

0.641

AC:

18774

AN:

29311

South Asian (SAS)

AF:

0.837

AC:

41422

AN:

49486

European-Finnish (FIN)

AF:

0.777

AC:

30516

AN:

39263

Middle Eastern (MID)

AF:

0.753

AC:

2122

AN:

2819

European-Non Finnish (NFE)

AF:

0.803

AC:

598690

AN:

745414

Other (OTH)

AF:

0.765

AC:

32106

AN:

41942

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

6118

12237

18355

24474

30592

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

16140

32280

48420

64560

80700

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

Data not reliable, filtered out with message: InbreedingCoeff

AF:

0.719

AC:

78895

AN:

109680

Hom.:

20457

Cov.:

AF XY:

0.715

AC XY:

22856

AN XY:

31964

show subpopulations

African (AFR)

AF:

0.627

AC:

18905

AN:

30154

American (AMR)

AF:

0.590

AC:

6119

AN:

10368

Ashkenazi Jewish (ASJ)

AF:

0.762

AC:

2002

AN:

2628

East Asian (EAS)

AF:

0.607

AC:

2077

AN:

3419

South Asian (SAS)

AF:

0.821

AC:

2057

AN:

2507

European-Finnish (FIN)

AF:

0.768

AC:

4378

AN:

5699

Middle Eastern (MID)

AF:

0.640

AC:

135

AN:

211

European-Non Finnish (NFE)

AF:

0.792

AC:

41595

AN:

52519

Other (OTH)

AF:

0.722

AC:

1084

AN:

1502

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.509

Heterozygous variant carriers

781

1562

2342

3123

3904

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:

0.757

Hom.:

54450

Bravo

AF:

0.698

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

3.6

(source)

DANN

Benign

0.46

PhyloP100

-0.24

PromoterAI

0.094

Neutral

(source)

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

Details are displayed if max score is > 0.2

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over