rs2285161

chr22-43852721-C-T

Variant summary

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

The NM_014351.4(SULT4A1):c.169+9493G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.203 in 151,094 control chromosomes in the GnomAD database, including 3,711 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 0.20 (3711 hom., cov: 29)
• Consequence: SULT4A1 NM_014351.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.43

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=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.455 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SULT4A1	NM_014351.4	c.169+9493G>A		intron_variant		ENST00000330884.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SULT4A1	ENST00000330884.9	c.169+9493G>A		intron_variant		1	NM_014351.4	P1
SULT4A1	ENST00000422525.1	c.169+9493G>A		intron_variant, NMD_transcript_variant		1
SULT4A1	ENST00000432404.5	c.169+9493G>A		intron_variant, NMD_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.203 AC: 30625 AN: 150976 Hom.: 3708 Cov.: 29

Gnomad AFR AF: 0.0944

Gnomad AMI AF: 0.232

Gnomad AMR AF: 0.295

Gnomad ASJ AF: 0.182

Gnomad EAS AF: 0.472

Gnomad SAS AF: 0.237

Gnomad FIN AF: 0.268

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.216

Gnomad OTH AF: 0.210

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

GnomAD4 genome AF: 0.203 AC: 30631 AN: 151094 Hom.: 3711 Cov.: 29 AF XY: 0.208 AC XY: 15316 AN XY: 73736

Gnomad4 AFR AF: 0.0943

Gnomad4 AMR AF: 0.295

Gnomad4 ASJ AF: 0.182

Gnomad4 EAS AF: 0.471

Gnomad4 SAS AF: 0.239

Gnomad4 FIN AF: 0.268

Gnomad4 NFE AF: 0.216

Gnomad4 OTH AF: 0.210

Alfa AF: 0.220 Hom.: 5391

Bravo AF: 0.209

Asia WGS AF: 0.349 AC: 1213 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	2.1
Dann	Benign	0.56

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: rs2285161; hg19: chr22-44248601;