rs2285167

Positions:

• chr22-43855309-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_014351.4(SULT4A1):​c.169+6905C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.133 in 152,236 control chromosomes in the GnomAD database, including 1,536 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 0.13 (1536 hom., cov: 32)
• Consequence: SULT4A1 NM_014351.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.547

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.202 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SULT4A1	NM_014351.4	c.169+6905C>T		intron_variant		ENST00000330884.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SULT4A1	ENST00000330884.9	c.169+6905C>T		intron_variant		1	NM_014351.4	P1
SULT4A1	ENST00000422525.1	c.169+6905C>T		intron_variant, NMD_transcript_variant		1
SULT4A1	ENST00000432404.5	c.169+6905C>T		intron_variant, NMD_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.133 AC: 20183 AN: 152118 Hom.: 1532 Cov.: 32

Gnomad AFR AF: 0.0425

Gnomad AMI AF: 0.125

Gnomad AMR AF: 0.119

Gnomad ASJ AF: 0.208

Gnomad EAS AF: 0.180

Gnomad SAS AF: 0.213

Gnomad FIN AF: 0.153

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.174

Gnomad OTH AF: 0.156

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

GnomAD4 genome AF: 0.133 AC: 20200 AN: 152236 Hom.: 1536 Cov.: 32 AF XY: 0.134 AC XY: 9945 AN XY: 74438

Gnomad4 AFR AF: 0.0426

Gnomad4 AMR AF: 0.119

Gnomad4 ASJ AF: 0.208

Gnomad4 EAS AF: 0.181

Gnomad4 SAS AF: 0.213

Gnomad4 FIN AF: 0.153

Gnomad4 NFE AF: 0.174

Gnomad4 OTH AF: 0.159

Alfa AF: 0.169 Hom.: 3073

Bravo AF: 0.122

Asia WGS AF: 0.203 AC: 706 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.1
DANN	Benign	0.48

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

Publications

LitVar

Other links and lift over

dbSNP: rs2285167; hg19: chr22-44251189;