chr4-69735474-A-C

Position:

• chr4-69735474-A-C

Variant summary

Our verdict is Benign. Variant got -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

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]

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
SULT1B1	NM_014465.4	c.376-1210T>G		intron_variant		ENST00000310613.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SULT1B1	ENST00000310613.8	c.376-1210T>G		intron_variant		1	NM_014465.4	P1
SULT1B1	ENST00000510821.1	c.376-1210T>G		intron_variant		3

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

Gnomad4 AFR AF: 0.883

Gnomad4 AMR AF: 0.933

Gnomad4 ASJ AF: 0.991

Gnomad4 EAS AF: 0.916

Gnomad4 SAS AF: 0.933

Gnomad4 FIN AF: 0.983

Gnomad4 NFE AF: 0.993

Gnomad4 OTH AF: 0.955

Alfa AF: 0.982 Hom.: 90918

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

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: rs1847365; hg19: chr4-70601192;