4-69750604-A-G

Variant names:

• chr4-69750604-A-G
• rs1354360
• NM_014465.4:c.278-786T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_014465.4(SULT1B1):​c.278-786T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.294 in 152,122 control chromosomes in the GnomAD database, including 7,691 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 0.29 (7691 hom., cov: 33)
• Consequence: SULT1B1 NM_014465.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.538
• Publications: 7 publications found

Genes affected

SULT1B1 (HGNC:17845): (sulfotransferase family 1B member 1) Sulfotransferase enzymes catalyze the sulfate conjugation of many hormones, neurotransmitters, drugs, and xenobiotic compounds. These cytosolic enzymes are different in their tissue distributions and substrate specificities. The gene structure (number and length of exons) is similar among family members. However, the total genomic length of this gene is greater than that of other SULT1 genes. [provided by RefSeq, Jul 2008]

SULT1B1 Gene-Disease associations (from GenCC):

• schizophrenia

  Inheritance: Unknown Classification: NO_KNOWN Submitted by: Labcorp Genetics (formerly Invitae)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.434 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014465.4. 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
	SULT1B1	NM_014465.4	MANE Select	c.278-786T>C		intron	N/A	NP_055280.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SULT1B1	ENST00000310613.8	TSL:1 MANE Select	c.278-786T>C		intron	N/A	ENSP00000308770.2
	SULT1B1	ENST00000510821.1	TSL:3	c.278-786T>C		intron	N/A	ENSP00000425464.1

Frequencies

GnomAD3 genomes AF: 0.295 AC: 44780 AN: 152004 Hom.: 7696 Cov.: 33

Gnomad AFR AF: 0.123

Gnomad AMI AF: 0.286

Gnomad AMR AF: 0.385

Gnomad ASJ AF: 0.383

Gnomad EAS AF: 0.251

Gnomad SAS AF: 0.450

Gnomad FIN AF: 0.341

Gnomad MID AF: 0.344

Gnomad NFE AF: 0.359

Gnomad OTH AF: 0.300

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

GnomAD4 genome AF: 0.294 AC: 44774 AN: 152122 Hom.: 7691 Cov.: 33 AF XY: 0.298 AC XY: 22151 AN XY: 74368

African (AFR) AF: 0.122 AC: 5084 AN: 41548

American (AMR) AF: 0.385 AC: 5880 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.383 AC: 1329 AN: 3470

East Asian (EAS) AF: 0.251 AC: 1300 AN: 5182

South Asian (SAS) AF: 0.450 AC: 2165 AN: 4816

European-Finnish (FIN) AF: 0.341 AC: 3604 AN: 10566

Middle Eastern (MID) AF: 0.342 AC: 100 AN: 292

European-Non Finnish (NFE) AF: 0.359 AC: 24422 AN: 67938

Other (OTH) AF: 0.298 AC: 630 AN: 2114

Alfa AF: 0.330 Hom.: 13845

Bravo AF: 0.288

Asia WGS AF: 0.288 AC: 1001 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.52
DANN	Benign	0.62
PhyloP100		-0.54
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: rs1354360; hg19: chr4-70616322;