22-43854690-A-G

Variant names:

• chr22-43854690-A-G
• rs138097
• NM_014351.4:c.169+7524T>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.169+7524T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.672 in 151,994 control chromosomes in the GnomAD database, including 35,517 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 0.67 (35517 hom., cov: 31)
• Consequence: SULT4A1 NM_014351.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.304
• Publications: 11 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=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.962 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SULT4A1	NM_014351.4	c.169+7524T>C		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+7524T>C		intron_variant	Intron 1 of 6	1	NM_014351.4	ENSP00000332565.4
SULT4A1	ENST00000422525.1	n.169+7524T>C		intron_variant	Intron 1 of 7	1		ENSP00000388285.1
SULT4A1	ENST00000432404.5	n.169+7524T>C		intron_variant	Intron 1 of 5	5		ENSP00000414220.1

Frequencies

GnomAD3 genomes AF: 0.672 AC: 102135 AN: 151876 Hom.: 35500 Cov.: 31

Gnomad AFR AF: 0.505

Gnomad AMI AF: 0.822

Gnomad AMR AF: 0.722

Gnomad ASJ AF: 0.679

Gnomad EAS AF: 0.985

Gnomad SAS AF: 0.889

Gnomad FIN AF: 0.746

Gnomad MID AF: 0.693

Gnomad NFE AF: 0.710

Gnomad OTH AF: 0.689

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

GnomAD4 genome AF: 0.672 AC: 102196 AN: 151994 Hom.: 35517 Cov.: 31 AF XY: 0.680 AC XY: 50512 AN XY: 74316

African (AFR) AF: 0.505 AC: 20896 AN: 41416

American (AMR) AF: 0.722 AC: 11039 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.679 AC: 2356 AN: 3468

East Asian (EAS) AF: 0.985 AC: 5081 AN: 5158

South Asian (SAS) AF: 0.889 AC: 4288 AN: 4822

European-Finnish (FIN) AF: 0.746 AC: 7898 AN: 10586

Middle Eastern (MID) AF: 0.697 AC: 205 AN: 294

European-Non Finnish (NFE) AF: 0.710 AC: 48226 AN: 67944

Other (OTH) AF: 0.692 AC: 1459 AN: 2108

Alfa AF: 0.691 Hom.: 16736

Bravo AF: 0.663

Asia WGS AF: 0.909 AC: 3161 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	4.9
DANN	Benign	0.36
PhyloP100		0.30
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: rs138097; hg19: chr22-44250570;