chr22-43826927-A-C

Variant names:

• chr22-43826927-A-C
• rs138060
• NM_014351.4:c.743-814T>G

Variant summary

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014351.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SULT4A1	NM_014351.4	MANE Select	c.743-814T>G		intron	N/A	NP_055166.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SULT4A1	ENST00000330884.9	TSL:1 MANE Select	c.743-814T>G		intron	N/A	ENSP00000332565.4
	SULT4A1	ENST00000422525.1	TSL:1	n.*86+587T>G		intron	N/A	ENSP00000388285.1
	SULT4A1	ENST00000432404.5	TSL:5	n.*384-814T>G		intron	N/A	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

African (AFR) AF: 0.510 AC: 8054 AN: 15784

American (AMR) AF: 0.391 AC: 385 AN: 984

Ashkenazi Jewish (ASJ) AF: 0.520 AC: 2678 AN: 5152

East Asian (EAS) AF: 0.477 AC: 1731 AN: 3630

South Asian (SAS) AF: 0.648 AC: 10666 AN: 16460

European-Finnish (FIN) AF: 0.536 AC: 148 AN: 276

Middle Eastern (MID) AF: 0.533 AC: 863 AN: 1620

European-Non Finnish (NFE) AF: 0.480 AC: 365642 AN: 761872

Other (OTH) AF: 0.502 AC: 13717 AN: 27298

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

African (AFR) AF: 0.496 AC: 20575 AN: 41506

American (AMR) AF: 0.433 AC: 6610 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.497 AC: 1725 AN: 3472

East Asian (EAS) AF: 0.489 AC: 2532 AN: 5176

South Asian (SAS) AF: 0.648 AC: 3120 AN: 4816

European-Finnish (FIN) AF: 0.492 AC: 5196 AN: 10558

Middle Eastern (MID) AF: 0.537 AC: 158 AN: 294

European-Non Finnish (NFE) AF: 0.494 AC: 33579 AN: 67960

Other (OTH) AF: 0.494 AC: 1045 AN: 2114

Alfa AF: 0.490 Hom.: 55616

Bravo AF: 0.481

Asia WGS AF: 0.559 AC: 1943 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.5
DANN	Benign	0.33
PhyloP100		-0.41
Mutation Taster		=99/1	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: rs138060; hg19: chr22-44222807;