Genetic Variant ENSG00000289755:n.424-131A>T (chr16-28620264-T-A) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The ENST00000562058.5(ENSG00000289755):n.424-131A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000362 in 829,872 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.000013 ( 0 hom., cov: 31)

Exomes 𝑓: 0.0000015 ( 0 hom. )

Consequence

ENSG00000289755
ENST00000562058.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.49

Publications

26 publications found

Variant links:

Genes affected

ENSG00000289755 (HGNC:):

ENSG00000289755 links:

SULT1A1 (HGNC:11453): (sulfotransferase family 1A member 1) Sulfotransferase enzymes catalyze the sulfate conjugation of many hormones, neurotransmitters, drugs, and xenobiotic compounds. These cytosolic enzymes are different in their tissue distributions and substrate specificities. The gene structure (number and length of exons) is similar among family members. This gene encodes one of two phenol sulfotransferases with thermostable enzyme activity. Multiple alternatively spliced variants that encode two isoforms have been identified for this gene. [provided by RefSeq, Jul 2008]

SULT1A1 links:

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (BayesDel_noAF=-1.03).

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	Protein
SULT1A1	NM_001394421.1 link	c.-409-131A>T	intron_variant	Intron 1 of 10	NP_001381350.1
SULT1A1	NM_001394422.1 link	c.-1208-131A>T	intron_variant	Intron 1 of 9	NP_001381351.1
SULT1A1	NM_001394423.1 link	c.-539-131A>T	intron_variant	Intron 1 of 11	NP_001381352.1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
ENSG00000289755	ENST00000562058.5 link	n.424-131A>T	intron_variant	Intron 1 of 9	1
ENSG00000289755	ENST00000564818.5 link	n.123-131A>T	intron_variant	Intron 1 of 10	1
ENSG00000289755	ENST00000563493.1 link	n.496-131A>T	intron_variant	Intron 1 of 8	5

Frequencies

GnomAD3 genomes

AF:

0.0000132

AC:

AN:

151898

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000131

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00

Gnomad OTH

AF:

0.00

GnomAD4 exome

AF:

0.00000147

AC:

AN:

677974

Hom.:

AF XY:

0.00000288

AC XY:

AN XY:

347664

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

16300

American (AMR)

AF:

0.00

AC:

AN:

21620

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

15098

East Asian (EAS)

AF:

0.00

AC:

AN:

29890

South Asian (SAS)

AF:

0.0000198

AC:

AN:

50498

European-Finnish (FIN)

AF:

0.00

AC:

AN:

40938

Middle Eastern (MID)

AF:

0.00

AC:

AN:

2274

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

469532

Other (OTH)

AF:

0.00

AC:

AN:

31824

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.425

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.0000132

AC:

AN:

151898

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

74188

show subpopulations

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR)

AF:

0.00

AC:

AN:

41320

American (AMR)

AF:

0.000131

AC:

AN:

15226

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3470

East Asian (EAS)

AF:

0.00

AC:

AN:

5194

South Asian (SAS)

AF:

0.00

AC:

AN:

4830

European-Finnish (FIN)

AF:

0.00

AC:

AN:

10558

Middle Eastern (MID)

AF:

0.00

AC:

AN:

316

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

67980

Other (OTH)

AF:

0.00

AC:

AN:

2092

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0.000000), which strongly suggests a high chance of mosaicism in these individuals.

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.400

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.00

Hom.:

72818

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

2.5

(source)

DANN

Benign

0.30

PhyloP100

-1.5

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over