rs1847365

Variant names:

• chr4-69735474-A-C
• rs1847365
• NM_014465.4:c.376-1210T>G

Your query was ambiguous. Multiple possible variants found:

• chr4-69735474-A-C
• chr4-69735474-A-G
• chr4-69735474-A-T

Variant summary

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

The NM_014465.4(SULT1B1):​c.376-1210T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.951 in 152,298 control chromosomes in the GnomAD database, including 69,013 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 0.95 (69013 hom., cov: 33)
• Consequence: SULT1B1 NM_014465.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.197
• Publications: 1 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=-1.03).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.987 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SULT1B1	NM_014465.4	c.376-1210T>G		intron_variant	Intron 4 of 7	ENST00000310613.8	NP_055280.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SULT1B1	ENST00000310613.8	c.376-1210T>G		intron_variant	Intron 4 of 7	1	NM_014465.4	ENSP00000308770.2
SULT1B1	ENST00000510821.1	c.376-1210T>G		intron_variant	Intron 5 of 5	3		ENSP00000425464.1

Frequencies

GnomAD3 genomes AF: 0.951 AC: 144697 AN: 152180 Hom.: 68965 Cov.: 33

Gnomad AFR AF: 0.882

Gnomad AMI AF: 0.980

Gnomad AMR AF: 0.933

Gnomad ASJ AF: 0.991

Gnomad EAS AF: 0.916

Gnomad SAS AF: 0.933

Gnomad FIN AF: 0.983

Gnomad MID AF: 0.949

Gnomad NFE AF: 0.993

Gnomad OTH AF: 0.956

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

GnomAD4 genome AF: 0.951 AC: 144805 AN: 152298 Hom.: 69013 Cov.: 33 AF XY: 0.949 AC XY: 70627 AN XY: 74460

African (AFR) AF: 0.883 AC: 36680 AN: 41556

American (AMR) AF: 0.933 AC: 14273 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.991 AC: 3440 AN: 3472

East Asian (EAS) AF: 0.916 AC: 4732 AN: 5166

South Asian (SAS) AF: 0.933 AC: 4501 AN: 4822

European-Finnish (FIN) AF: 0.983 AC: 10442 AN: 10624

Middle Eastern (MID) AF: 0.946 AC: 278 AN: 294

European-Non Finnish (NFE) AF: 0.993 AC: 67545 AN: 68034

Other (OTH) AF: 0.955 AC: 2020 AN: 2116

Alfa AF: 0.978 Hom.: 115757

Bravo AF: 0.944

Asia WGS AF: 0.923 AC: 3212 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.50
PhyloP100		-0.20
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: rs1847365; hg19: chr4-70601192;