NM_014351.4:c.169+6446G>A

Variant names:

• chr22-43855768-C-T
• rs470091
• NM_014351.4:c.169+6446G>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+6446G>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 151,960 control chromosomes in the GnomAD database, including 4,447 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 (4447 hom., cov: 31)
• Consequence: SULT4A1 NM_014351.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.19
• Publications: 6 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=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.315 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SULT4A1	NM_014351.4	c.169+6446G>A		intron_variant	Intron 1 of 6	ENST00000330884.9	NP_055166.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SULT4A1	ENST00000330884.9	c.169+6446G>A		intron_variant	Intron 1 of 6	1	NM_014351.4	ENSP00000332565.4
SULT4A1	ENST00000422525.1	n.169+6446G>A		intron_variant	Intron 1 of 7	1		ENSP00000388285.1
SULT4A1	ENST00000432404.5	n.169+6446G>A		intron_variant	Intron 1 of 5	5		ENSP00000414220.1

Frequencies

GnomAD3 genomes AF: 0.236 AC: 35801 AN: 151842 Hom.: 4442 Cov.: 31

Gnomad AFR AF: 0.320

Gnomad AMI AF: 0.314

Gnomad AMR AF: 0.179

Gnomad ASJ AF: 0.218

Gnomad EAS AF: 0.0548

Gnomad SAS AF: 0.229

Gnomad FIN AF: 0.225

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.214

Gnomad OTH AF: 0.218

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

GnomAD4 genome AF: 0.236 AC: 35829 AN: 151960 Hom.: 4447 Cov.: 31 AF XY: 0.234 AC XY: 17361 AN XY: 74288

African (AFR) AF: 0.319 AC: 13221 AN: 41396

American (AMR) AF: 0.179 AC: 2735 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.218 AC: 755 AN: 3470

East Asian (EAS) AF: 0.0549 AC: 284 AN: 5170

South Asian (SAS) AF: 0.229 AC: 1100 AN: 4808

European-Finnish (FIN) AF: 0.225 AC: 2373 AN: 10562

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

European-Non Finnish (NFE) AF: 0.214 AC: 14546 AN: 67962

Other (OTH) AF: 0.219 AC: 461 AN: 2106

Alfa AF: 0.217 Hom.: 1948

Bravo AF: 0.233

Asia WGS AF: 0.161 AC: 565 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	12
DANN	Benign	0.82
PhyloP100		1.2
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: rs470091; hg19: chr22-44251648;