22-43843619-T-C

Variant names:

• chr22-43843619-T-C
• rs138079
• NM_014351.4:c.170-1687A>G

Variant summary

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

The NM_014351.4(SULT4A1):​c.170-1687A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.888 in 152,236 control chromosomes in the GnomAD database, including 60,249 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 0.89 (60249 hom., cov: 32)
• Consequence: SULT4A1 NM_014351.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.449
• 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=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.972 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SULT4A1	NM_014351.4	MANE Select	c.170-1687A>G		intron	N/A	NP_055166.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SULT4A1	ENST00000330884.9	TSL:1 MANE Select	c.170-1687A>G		intron	N/A	ENSP00000332565.4
	SULT4A1	ENST00000422525.1	TSL:1	n.170-1687A>G		intron	N/A	ENSP00000388285.1
	SULT4A1	ENST00000432404.5	TSL:5	n.170-3594A>G		intron	N/A	ENSP00000414220.1

Frequencies

GnomAD3 genomes AF: 0.888 AC: 135083 AN: 152118 Hom.: 60184 Cov.: 32

Gnomad AFR AF: 0.938

Gnomad AMI AF: 0.936

Gnomad AMR AF: 0.880

Gnomad ASJ AF: 0.822

Gnomad EAS AF: 0.994

Gnomad SAS AF: 0.949

Gnomad FIN AF: 0.921

Gnomad MID AF: 0.822

Gnomad NFE AF: 0.846

Gnomad OTH AF: 0.866

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

GnomAD4 genome AF: 0.888 AC: 135208 AN: 152236 Hom.: 60249 Cov.: 32 AF XY: 0.892 AC XY: 66389 AN XY: 74436

African (AFR) AF: 0.938 AC: 38957 AN: 41546

American (AMR) AF: 0.880 AC: 13459 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.822 AC: 2854 AN: 3472

East Asian (EAS) AF: 0.994 AC: 5137 AN: 5166

South Asian (SAS) AF: 0.950 AC: 4587 AN: 4830

European-Finnish (FIN) AF: 0.921 AC: 9777 AN: 10610

Middle Eastern (MID) AF: 0.839 AC: 245 AN: 292

European-Non Finnish (NFE) AF: 0.846 AC: 57508 AN: 68000

Other (OTH) AF: 0.866 AC: 1830 AN: 2112

Alfa AF: 0.882 Hom.: 24951

Bravo AF: 0.886

Asia WGS AF: 0.968 AC: 3365 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.7
DANN	Benign	0.71
PhyloP100		-0.45
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: rs138079; hg19: chr22-44239499;