rs2285164

Positions:

• chr22-43854025-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+8189C>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 152,184 control chromosomes in the GnomAD database, including 4,769 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 (4769 hom., cov: 33)
• Consequence: SULT4A1 NM_014351.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.398

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=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.443 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SULT4A1	NM_014351.4	c.169+8189C>T		intron_variant		ENST00000330884.9	NP_055166.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SULT4A1	ENST00000330884.9	c.169+8189C>T		intron_variant		1	NM_014351.4	ENSP00000332565	P1
SULT4A1	ENST00000422525.1	c.169+8189C>T		intron_variant, NMD_transcript_variant		1		ENSP00000388285
SULT4A1	ENST00000432404.5	c.169+8189C>T		intron_variant, NMD_transcript_variant		5		ENSP00000414220

Frequencies

GnomAD3 genomes AF: 0.232 AC: 35277 AN: 152066 Hom.: 4763 Cov.: 33

Gnomad AFR AF: 0.0887

Gnomad AMI AF: 0.274

Gnomad AMR AF: 0.246

Gnomad ASJ AF: 0.276

Gnomad EAS AF: 0.458

Gnomad SAS AF: 0.418

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: 35296 AN: 152184 Hom.: 4769 Cov.: 33 AF XY: 0.236 AC XY: 17590 AN XY: 74420

Gnomad4 AFR AF: 0.0887

Gnomad4 AMR AF: 0.246

Gnomad4 ASJ AF: 0.276

Gnomad4 EAS AF: 0.458

Gnomad4 SAS AF: 0.417

Gnomad4 FIN AF: 0.252

Gnomad4 NFE AF: 0.279

Gnomad4 OTH AF: 0.260

Alfa AF: 0.274 Hom.: 7765

Bravo AF: 0.221

Asia WGS AF: 0.391 AC: 1357 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	0.67
DANN	Benign	0.44

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: rs2285164; hg19: chr22-44249905;