rs138060

Positions:

• chr22-43826927-A-C

Variant summary

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

The NM_014351.4(SULT4A1):​c.743-814T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.486 in 985,146 control chromosomes in the GnomAD database, including 116,955 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 0.49 (18785 hom., cov: 33)
  • Exomes 𝑓: 0.48 (98170 hom.)
• Consequence: SULT4A1 NM_014351.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.409

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=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.629 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SULT4A1	NM_014351.4	c.743-814T>G		intron_variant		ENST00000330884.9	NP_055166.1
SULT4A1	XM_011530121.2	c.404-814T>G		intron_variant			XP_011528423.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SULT4A1	ENST00000330884.9	c.743-814T>G		intron_variant		1	NM_014351.4	ENSP00000332565.4
SULT4A1	ENST00000422525.1	n.*86+587T>G		intron_variant		1		ENSP00000388285.1
SULT4A1	ENST00000432404.5	n.*384-814T>G		intron_variant		5		ENSP00000414220.1

Frequencies

GnomAD3 genomes AF: 0.494 AC: 75003 AN: 151952 Hom.: 18759 Cov.: 33

Gnomad AFR AF: 0.495

Gnomad AMI AF: 0.590

Gnomad AMR AF: 0.433

Gnomad ASJ AF: 0.497

Gnomad EAS AF: 0.489

Gnomad SAS AF: 0.649

Gnomad FIN AF: 0.492

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.494

Gnomad OTH AF: 0.491

GnomAD4 exome AF: 0.485 AC: 403884 AN: 833076 Hom.: 98170 Cov.: 34 AF XY: 0.485 AC XY: 186419 AN XY: 384696

Gnomad4 AFR exome AF: 0.510

Gnomad4 AMR exome AF: 0.391

Gnomad4 ASJ exome AF: 0.520

Gnomad4 EAS exome AF: 0.477

Gnomad4 SAS exome AF: 0.648

Gnomad4 FIN exome AF: 0.536

Gnomad4 NFE exome AF: 0.480

Gnomad4 OTH exome AF: 0.502

GnomAD4 genome AF: 0.494 AC: 75076 AN: 152070 Hom.: 18785 Cov.: 33 AF XY: 0.495 AC XY: 36794 AN XY: 74312

Gnomad4 AFR AF: 0.496

Gnomad4 AMR AF: 0.433

Gnomad4 ASJ AF: 0.497

Gnomad4 EAS AF: 0.489

Gnomad4 SAS AF: 0.648

Gnomad4 FIN AF: 0.492

Gnomad4 NFE AF: 0.494

Gnomad4 OTH AF: 0.494

Alfa AF: 0.491 Hom.: 24516

Bravo AF: 0.481

Asia WGS AF: 0.559 AC: 1943 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.5
DANN	Benign	0.33

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: rs138060; hg19: chr22-44222807;