rs11647881

Positions:

• chr16-28594852-C-A

Variant summary

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

The NM_001054.4(SULT1A2):​c.372+515G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.108 in 137,228 control chromosomes in the GnomAD database, including 843 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 0.11 (843 hom., cov: 25)
• Consequence: SULT1A2 NM_001054.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.719

Genes affected

SULT1A2 (HGNC:11454): (sulfotransferase family 1A member 2) 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. Two alternatively spliced variants that encode the same protein have been described. [provided by RefSeq, Jul 2008]

ENSG00000288656 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.125 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SULT1A2	NM_001054.4	c.372+515G>T		intron_variant		ENST00000335715.9	NP_001045.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SULT1A2	ENST00000335715.9	c.372+515G>T		intron_variant		1	NM_001054.4	ENSP00000338742.4

Frequencies

GnomAD3 genomes AF: 0.108 AC: 14839 AN: 137148 Hom.: 843 Cov.: 25

Gnomad AFR AF: 0.0713

Gnomad AMI AF: 0.265

Gnomad AMR AF: 0.120

Gnomad ASJ AF: 0.168

Gnomad EAS AF: 0.00325

Gnomad SAS AF: 0.102

Gnomad FIN AF: 0.106

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.128

Gnomad OTH AF: 0.136

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.108 AC: 14842 AN: 137228 Hom.: 843 Cov.: 25 AF XY: 0.107 AC XY: 7036 AN XY: 65668

Gnomad4 AFR AF: 0.0713

Gnomad4 AMR AF: 0.119

Gnomad4 ASJ AF: 0.168

Gnomad4 EAS AF: 0.00325

Gnomad4 SAS AF: 0.102

Gnomad4 FIN AF: 0.106

Gnomad4 NFE AF: 0.128

Gnomad4 OTH AF: 0.135

Alfa AF: 0.101 Hom.: 87

Asia WGS AF: 0.0480 AC: 168 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.48
DANN	Benign	0.35

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs11647881; hg19: chr16-28606173;