Genetic Variant NM_001055.4:c.-4-392G>A (chr16-28609251-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001055.4(SULT1A1):c.-4-392G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.47 in 1,242,994 control chromosomes in the GnomAD database, including 134,960 homozygotes. 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 0.45 ( 14814 hom., cov: 38)

Exomes 𝑓: 0.47 ( 120146 hom. )

Consequence

SULT1A1
NM_001055.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.336

Variant links:

Genes affected

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:

ENSG00000289755 (HGNC:):

ENSG00000289755 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-1.01).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.49 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SULT1A1	NM_001055.4 link	c.-4-392G>A		intron_variant	Intron 1 of 7	ENST00000314752.12	NP_001046.2	P50225-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SULT1A1	ENST00000314752.12 link	c.-4-392G>A		intron_variant	Intron 1 of 7	1	NM_001055.4	ENSP00000321988.7		P50225-1

Frequencies

GnomAD3 genomes

AF:

0.449

AC:

67576

AN:

150432

Hom.:

14796

Cov.:

show subpopulations

Gnomad AFR

AF:

0.356

Gnomad AMI

AF:

0.417

Gnomad AMR

AF:

0.481

Gnomad ASJ

AF:

0.410

Gnomad EAS

AF:

0.441

Gnomad SAS

AF:

0.308

Gnomad FIN

AF:

0.571

Gnomad MID

AF:

0.342

Gnomad NFE

AF:

0.494

Gnomad OTH

AF:

0.421

GnomAD4 exome

AF:

0.473

AC:

517035

AN:

1092444

Hom.:

120146

Cov.:

AF XY:

0.469

AC XY:

247950

AN XY:

528860

show subpopulations

Gnomad4 AFR exome

AF:

0.341

Gnomad4 AMR exome

AF:

0.534

Gnomad4 ASJ exome

AF:

0.407

Gnomad4 EAS exome

AF:

0.462

Gnomad4 SAS exome

AF:

0.316

Gnomad4 FIN exome

AF:

0.558

Gnomad4 NFE exome

AF:

0.488

Gnomad4 OTH exome

AF:

0.457

GnomAD4 genome

AF:

0.449

AC:

67648

AN:

150550

Hom.:

14814

Cov.:

AF XY:

0.451

AC XY:

33161

AN XY:

73544

show subpopulations

Gnomad4 AFR

AF:

0.356

Gnomad4 AMR

AF:

0.482

Gnomad4 ASJ

AF:

0.410

Gnomad4 EAS

AF:

0.441

Gnomad4 SAS

AF:

0.308

Gnomad4 FIN

AF:

0.571

Gnomad4 NFE

AF:

0.494

Gnomad4 OTH

AF:

0.423

Alfa

AF:

0.315

Hom.:

685

Asia WGS

AF:

0.396

AC:

1375

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

2.2

DANN

Benign

0.50

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over