4-69750604-A-G

Position:

• chr4-69750604-A-G

Variant summary

Our verdict is Benign. Variant got -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

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=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.434 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SULT1B1	NM_014465.4	c.278-786T>C		intron_variant		ENST00000310613.8	NP_055280.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SULT1B1	ENST00000310613.8	c.278-786T>C		intron_variant		1	NM_014465.4	ENSP00000308770.2
SULT1B1	ENST00000510821.1	c.278-786T>C		intron_variant		3		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

Gnomad4 AFR AF: 0.122

Gnomad4 AMR AF: 0.385

Gnomad4 ASJ AF: 0.383

Gnomad4 EAS AF: 0.251

Gnomad4 SAS AF: 0.450

Gnomad4 FIN AF: 0.341

Gnomad4 NFE AF: 0.359

Gnomad4 OTH AF: 0.298

Alfa AF: 0.336 Hom.: 11094

Bravo AF: 0.288

Asia WGS AF: 0.288 AC: 1001 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.52
DANN	Benign	0.62

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: rs1354360; hg19: chr4-70616322;