chr16-28594852-C-A

Variant names:

• chr16-28594852-C-A
• rs11647881
• NM_001054.4:c.372+515G>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
SULT1A2	NM_001054.4	c.372+515G>T		intron_variant	Intron 4 of 7	ENST00000335715.9	NP_001045.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SULT1A2	ENST00000335715.9	c.372+515G>T		intron_variant	Intron 4 of 7	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

African (AFR) AF: 0.0713 AC: 2596 AN: 36418

American (AMR) AF: 0.119 AC: 1506 AN: 12616

Ashkenazi Jewish (ASJ) AF: 0.168 AC: 571 AN: 3394

East Asian (EAS) AF: 0.00325 AC: 14 AN: 4310

South Asian (SAS) AF: 0.102 AC: 419 AN: 4098

European-Finnish (FIN) AF: 0.106 AC: 832 AN: 7858

Middle Eastern (MID) AF: 0.207 AC: 51 AN: 246

European-Non Finnish (NFE) AF: 0.128 AC: 8371 AN: 65540

Other (OTH) AF: 0.135 AC: 255 AN: 1892

Alfa AF: 0.0992 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
PhyloP100		-0.72
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs11647881; hg19: chr16-28606173;