22-43857209-C-T

Position:

• chr22-43857209-C-T

Variant summary

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

The NM_014351.4(SULT4A1):​c.169+5005G>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 151,676 control chromosomes in the GnomAD database, including 4,419 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 (4419 hom., cov: 31)
• Consequence: SULT4A1 NM_014351.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.913

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]

SULT4A1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.312 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SULT4A1	NM_014351.4	c.169+5005G>A		intron_variant		ENST00000330884.9	NP_055166.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SULT4A1	ENST00000330884.9	c.169+5005G>A		intron_variant		1	NM_014351.4	ENSP00000332565.4
SULT4A1	ENST00000422525.1	n.169+5005G>A		intron_variant		1		ENSP00000388285.1
SULT4A1	ENST00000432404.5	n.169+5005G>A		intron_variant		5		ENSP00000414220.1

Frequencies

GnomAD3 genomes AF: 0.236 AC: 35696 AN: 151558 Hom.: 4415 Cov.: 31

Gnomad AFR AF: 0.317

Gnomad AMI AF: 0.315

Gnomad AMR AF: 0.179

Gnomad ASJ AF: 0.225

Gnomad EAS AF: 0.0548

Gnomad SAS AF: 0.228

Gnomad FIN AF: 0.226

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.215

Gnomad OTH AF: 0.219

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

GnomAD4 genome AF: 0.236 AC: 35722 AN: 151676 Hom.: 4419 Cov.: 31 AF XY: 0.233 AC XY: 17301 AN XY: 74110

Gnomad4 AFR AF: 0.317

Gnomad4 AMR AF: 0.179

Gnomad4 ASJ AF: 0.225

Gnomad4 EAS AF: 0.0550

Gnomad4 SAS AF: 0.227

Gnomad4 FIN AF: 0.226

Gnomad4 NFE AF: 0.215

Gnomad4 OTH AF: 0.220

Alfa AF: 0.201 Hom.: 3287

Bravo AF: 0.232

Asia WGS AF: 0.160 AC: 560 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.19
DANN	Benign	0.64

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: rs138102; hg19: chr22-44253089;