rs2285162

Variant names:

• chr22-43853583-C-A
• rs2285162
• NM_014351.4:c.169+8631G>T

Variant summary

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

The NM_014351.4(SULT4A1):​c.169+8631G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.232 in 152,198 control chromosomes in the GnomAD database, including 4,773 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 0.23 (4773 hom., cov: 33)
• Consequence: SULT4A1 NM_014351.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.25
• Publications: 10 publications found

Genes affected

SULT4A1 (HGNC:14903): (sulfotransferase family 4A member 1) This gene encodes a member of the sulfotransferase family. The encoded protein is a brain-specific sulfotransferase believed to be involved in the metabolism of neurotransmitters. Polymorphisms in this gene may be associated with susceptibility to schizophrenia. [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=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.442 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SULT4A1	NM_014351.4	c.169+8631G>T		intron_variant	Intron 1 of 6	ENST00000330884.9	NP_055166.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SULT4A1	ENST00000330884.9	c.169+8631G>T		intron_variant	Intron 1 of 6	1	NM_014351.4	ENSP00000332565.4
SULT4A1	ENST00000422525.1	n.169+8631G>T		intron_variant	Intron 1 of 7	1		ENSP00000388285.1
SULT4A1	ENST00000432404.5	n.169+8631G>T		intron_variant	Intron 1 of 5	5		ENSP00000414220.1

Frequencies

GnomAD3 genomes AF: 0.232 AC: 35273 AN: 152080 Hom.: 4766 Cov.: 33

Gnomad AFR AF: 0.0887

Gnomad AMI AF: 0.273

Gnomad AMR AF: 0.246

Gnomad ASJ AF: 0.276

Gnomad EAS AF: 0.456

Gnomad SAS AF: 0.419

Gnomad FIN AF: 0.252

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.279

Gnomad OTH AF: 0.257

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

GnomAD4 genome AF: 0.232 AC: 35293 AN: 152198 Hom.: 4773 Cov.: 33 AF XY: 0.236 AC XY: 17576 AN XY: 74408

African (AFR) AF: 0.0888 AC: 3689 AN: 41548

American (AMR) AF: 0.246 AC: 3763 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.276 AC: 957 AN: 3470

East Asian (EAS) AF: 0.457 AC: 2354 AN: 5152

South Asian (SAS) AF: 0.418 AC: 2022 AN: 4832

European-Finnish (FIN) AF: 0.252 AC: 2665 AN: 10592

Middle Eastern (MID) AF: 0.272 AC: 80 AN: 294

European-Non Finnish (NFE) AF: 0.279 AC: 18966 AN: 67994

Other (OTH) AF: 0.260 AC: 549 AN: 2112

Alfa AF: 0.249 Hom.: 886

Bravo AF: 0.221

Asia WGS AF: 0.393 AC: 1364 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.57
DANN	Benign	0.58
PhyloP100		-1.2
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: rs2285162; hg19: chr22-44249463;