chr22-43837546-A-G

Variant names:

• chr22-43837546-A-G
• rs7291934
• NM_014351.4:c.508+1321T>C

Variant summary

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

The NM_014351.4(SULT4A1):​c.508+1321T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.152 in 152,220 control chromosomes in the GnomAD database, including 1,889 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 0.15 (1889 hom., cov: 33)
• Consequence: SULT4A1 NM_014351.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.898
• Publications: 3 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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.212 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SULT4A1	NM_014351.4	c.508+1321T>C		intron_variant	Intron 4 of 6	ENST00000330884.9	NP_055166.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SULT4A1	ENST00000330884.9	c.508+1321T>C		intron_variant	Intron 4 of 6	1	NM_014351.4	ENSP00000332565.4
SULT4A1	ENST00000422525.1	n.508+1321T>C		intron_variant	Intron 4 of 7	1		ENSP00000388285.1
SULT4A1	ENST00000432404.5	n.*149+1321T>C		intron_variant	Intron 3 of 5	5		ENSP00000414220.1
SULT4A1	ENST00000475131.1	n.47+1321T>C		intron_variant	Intron 1 of 2	4

Frequencies

GnomAD3 genomes AF: 0.152 AC: 23127 AN: 152102 Hom.: 1883 Cov.: 33

Gnomad AFR AF: 0.215

Gnomad AMI AF: 0.115

Gnomad AMR AF: 0.136

Gnomad ASJ AF: 0.141

Gnomad EAS AF: 0.00926

Gnomad SAS AF: 0.0592

Gnomad FIN AF: 0.175

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.133

Gnomad OTH AF: 0.131

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

GnomAD4 genome AF: 0.152 AC: 23170 AN: 152220 Hom.: 1889 Cov.: 33 AF XY: 0.151 AC XY: 11224 AN XY: 74422

African (AFR) AF: 0.215 AC: 8946 AN: 41518

American (AMR) AF: 0.136 AC: 2083 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.141 AC: 491 AN: 3472

East Asian (EAS) AF: 0.00928 AC: 48 AN: 5172

South Asian (SAS) AF: 0.0595 AC: 287 AN: 4826

European-Finnish (FIN) AF: 0.175 AC: 1854 AN: 10612

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.133 AC: 9051 AN: 68006

Other (OTH) AF: 0.129 AC: 273 AN: 2110

Alfa AF: 0.107 Hom.: 226

Bravo AF: 0.151

Asia WGS AF: 0.0460 AC: 162 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.29
DANN	Benign	0.49
PhyloP100		-0.90
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: rs7291934; hg19: chr22-44233426;