16-28618867-T-C

Variant names:

• chr16-28618867-T-C
• rs7192559
• ENST00000562058.5:n.494+1196A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001394421.1(SULT1A1):​c.-339+1196A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.907 in 152,234 control chromosomes in the GnomAD database, including 64,209 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 0.91 (64209 hom., cov: 32)
• Consequence: SULT1A1 NM_001394421.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.58
• Publications: 5 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.992 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001394421.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SULT1A1	NM_001394421.1		c.-339+1196A>G		intron	N/A	NP_001381350.1	P50225-1
	SULT1A1	NM_001394422.1		c.-1138+1196A>G		intron	N/A	NP_001381351.1	P50225-1
	SULT1A1	NM_001394423.1		c.-469+1196A>G		intron	N/A	NP_001381352.1	P50225-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000289755	ENST00000562058.5	TSL:1	n.494+1196A>G		intron	N/A
	ENSG00000289755	ENST00000564818.5	TSL:1	n.193+1196A>G		intron	N/A
	ENSG00000289755	ENST00000563493.1	TSL:5	n.566+1196A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.908 AC: 138046 AN: 152116 Hom.: 64179 Cov.: 32

Gnomad AFR AF: 0.680

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.962

Gnomad ASJ AF: 0.991

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.999

Gnomad FIN AF: 1.00

Gnomad MID AF: 0.991

Gnomad NFE AF: 0.999

Gnomad OTH AF: 0.935

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

GnomAD4 genome AF: 0.907 AC: 138131 AN: 152234 Hom.: 64209 Cov.: 32 AF XY: 0.912 AC XY: 67917 AN XY: 74430

African (AFR) AF: 0.680 AC: 28212 AN: 41478

American (AMR) AF: 0.962 AC: 14714 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.991 AC: 3440 AN: 3470

East Asian (EAS) AF: 1.00 AC: 5194 AN: 5194

South Asian (SAS) AF: 0.999 AC: 4827 AN: 4830

European-Finnish (FIN) AF: 1.00 AC: 10617 AN: 10618

Middle Eastern (MID) AF: 0.990 AC: 291 AN: 294

European-Non Finnish (NFE) AF: 0.999 AC: 67946 AN: 68034

Other (OTH) AF: 0.936 AC: 1980 AN: 2116

Alfa AF: 0.947 Hom.: 117717

Bravo AF: 0.895

Asia WGS AF: 0.979 AC: 3405 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	4.2
DANN	Benign	0.27
PhyloP100		-1.6
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs7192559; hg19: chr16-28630188;