22-43857209-C-T

Variant names:

• chr22-43857209-C-T
• rs138102
• NM_014351.4:c.169+5005G>A

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+5005G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.236 in 151,676 control chromosomes in the GnomAD database, including 4,419 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 0.24 (4419 hom., cov: 31)
• Consequence: SULT4A1 NM_014351.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.913
• Publications: 8 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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.312 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014351.4. 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
	SULT4A1	NM_014351.4	MANE Select	c.169+5005G>A		intron	N/A	NP_055166.1	Q9BR01-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SULT4A1	ENST00000330884.9	TSL:1 MANE Select	c.169+5005G>A		intron	N/A	ENSP00000332565.4	Q9BR01-1
	SULT4A1	ENST00000422525.1	TSL:1	n.169+5005G>A		intron	N/A	ENSP00000388285.1	Q9BR01-2
	SULT4A1	ENST00000884819.1		c.169+5005G>A		intron	N/A	ENSP00000554878.1

Frequencies

GnomAD3 genomes AF: 0.236 AC: 35696 AN: 151558 Hom.: 4415 Cov.: 31

Gnomad AFR AF: 0.317

Gnomad AMI AF: 0.315

Gnomad AMR AF: 0.179

Gnomad ASJ AF: 0.225

Gnomad EAS AF: 0.0548

Gnomad SAS AF: 0.228

Gnomad FIN AF: 0.226

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.215

Gnomad OTH AF: 0.219

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

GnomAD4 genome AF: 0.236 AC: 35722 AN: 151676 Hom.: 4419 Cov.: 31 AF XY: 0.233 AC XY: 17301 AN XY: 74110

African (AFR) AF: 0.317 AC: 13082 AN: 41312

American (AMR) AF: 0.179 AC: 2729 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.225 AC: 778 AN: 3464

East Asian (EAS) AF: 0.0550 AC: 284 AN: 5166

South Asian (SAS) AF: 0.227 AC: 1089 AN: 4794

European-Finnish (FIN) AF: 0.226 AC: 2375 AN: 10488

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.215 AC: 14568 AN: 67900

Other (OTH) AF: 0.220 AC: 462 AN: 2104

Alfa AF: 0.209 Hom.: 5814

Bravo AF: 0.232

Asia WGS AF: 0.160 AC: 560 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.19
DANN	Benign	0.64
PhyloP100		-0.91
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: rs138102; hg19: chr22-44253089;