16-28620264-T-G

Position:

• chr16-28620264-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001394421.1(SULT1A1):​c.-409-131A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.638 in 827,720 control chromosomes in the GnomAD database, including 172,672 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 0.60 (28469 hom., cov: 31)
  • Exomes 𝑓: 0.65 (144203 hom.)
• Consequence: SULT1A1 NM_001394421.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.49

Genes affected

ENSG00000289755 (HGNC:):

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.915 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SULT1A1	NM_001394421.1	c.-409-131A>C		intron_variant			NP_001381350.1
SULT1A1	NM_001394422.1	c.-1208-131A>C		intron_variant			NP_001381351.1
SULT1A1	NM_001394423.1	c.-539-131A>C		intron_variant			NP_001381352.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000289755	ENST00000562058.5	n.424-131A>C		intron_variant		1
ENSG00000289755	ENST00000564818.5	n.123-131A>C		intron_variant		1
ENSG00000289755	ENST00000563493.1	n.496-131A>C		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.601 AC: 91302 AN: 151824 Hom.: 28460 Cov.: 31

Gnomad AFR AF: 0.479

Gnomad AMI AF: 0.811

Gnomad AMR AF: 0.631

Gnomad ASJ AF: 0.693

Gnomad EAS AF: 0.937

Gnomad SAS AF: 0.776

Gnomad FIN AF: 0.548

Gnomad MID AF: 0.801

Gnomad NFE AF: 0.629

Gnomad OTH AF: 0.660

GnomAD4 exome AF: 0.646 AC: 436795 AN: 675778 Hom.: 144203 AF XY: 0.651 AC XY: 225576 AN XY: 346586

Gnomad4 AFR exome AF: 0.474

Gnomad4 AMR exome AF: 0.581

Gnomad4 ASJ exome AF: 0.701

Gnomad4 EAS exome AF: 0.918

Gnomad4 SAS exome AF: 0.770

Gnomad4 FIN exome AF: 0.555

Gnomad4 NFE exome AF: 0.629

Gnomad4 OTH exome AF: 0.659

GnomAD4 genome AF: 0.601 AC: 91341 AN: 151942 Hom.: 28469 Cov.: 31 AF XY: 0.607 AC XY: 45086 AN XY: 74278

Gnomad4 AFR AF: 0.479

Gnomad4 AMR AF: 0.631

Gnomad4 ASJ AF: 0.693

Gnomad4 EAS AF: 0.937

Gnomad4 SAS AF: 0.777

Gnomad4 FIN AF: 0.548

Gnomad4 NFE AF: 0.629

Gnomad4 OTH AF: 0.665

Alfa AF: 0.620 Hom.: 21721

Bravo AF: 0.602

Asia WGS AF: 0.803 AC: 2794 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	2.7
DANN	Benign	0.24

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1968752; hg19: chr16-28631585;