rs470089

Positions:

• chr22-43852624-G-A

Variant summary

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

The NM_014351.4(SULT4A1):​c.169+9590C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.233 in 151,872 control chromosomes in the GnomAD database, including 4,333 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 (4333 hom., cov: 30)
• Consequence: SULT4A1 NM_014351.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.56

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.307 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SULT4A1	NM_014351.4	c.169+9590C>T		intron_variant		ENST00000330884.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SULT4A1	ENST00000330884.9	c.169+9590C>T		intron_variant		1	NM_014351.4	P1
SULT4A1	ENST00000422525.1	c.169+9590C>T		intron_variant, NMD_transcript_variant		1
SULT4A1	ENST00000432404.5	c.169+9590C>T		intron_variant, NMD_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.233 AC: 35426 AN: 151754 Hom.: 4331 Cov.: 30

Gnomad AFR AF: 0.312

Gnomad AMI AF: 0.315

Gnomad AMR AF: 0.179

Gnomad ASJ AF: 0.217

Gnomad EAS AF: 0.0553

Gnomad SAS AF: 0.227

Gnomad FIN AF: 0.225

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.214

Gnomad OTH AF: 0.216

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

GnomAD4 genome AF: 0.233 AC: 35441 AN: 151872 Hom.: 4333 Cov.: 30 AF XY: 0.231 AC XY: 17150 AN XY: 74218

Gnomad4 AFR AF: 0.311

Gnomad4 AMR AF: 0.178

Gnomad4 ASJ AF: 0.217

Gnomad4 EAS AF: 0.0554

Gnomad4 SAS AF: 0.226

Gnomad4 FIN AF: 0.225

Gnomad4 NFE AF: 0.214

Gnomad4 OTH AF: 0.218

Alfa AF: 0.212 Hom.: 4961

Bravo AF: 0.230

Asia WGS AF: 0.158 AC: 555 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.13
DANN	Benign	0.50

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: rs470089; hg19: chr22-44248504;