Variant 4-69754755-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2

The NM_014465.4(SULT1B1):c.192T>C(p.Asp64=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00585 in 1,612,832 control chromosomes in the GnomAD database, including 44 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0041 ( 0 hom., cov: 33)

Exomes 𝑓: 0.0060 ( 44 hom. )

Consequence

SULT1B1
NM_014465.4 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.397

Variant links:

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 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -17 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.56).

BP6

Variant 4-69754755-A-G is Benign according to our data. Variant chr4-69754755-A-G is described in ClinVar as [Benign]. Clinvar id is 787615.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=0.397 with no splicing effect.

BS2

High Homozygotes in GnomAdExome4 at 44 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SULT1B1	NM_014465.4 linkuse as main transcript	c.192T>C	p.Asp64=	synonymous_variant	3/8	ENST00000310613.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris
SULT1B1	ENST00000310613.8 linkuse as main transcript	c.192T>C	p.Asp64=	synonymous_variant	3/8	1	NM_014465.4	P1
SULT1B1	ENST00000510821.1 linkuse as main transcript	c.192T>C	p.Asp64=	synonymous_variant	4/6	3
SULT1B1	ENST00000512870.1 linkuse as main transcript	c.135T>C	p.Asp45=	synonymous_variant	5/5	3

Frequencies

GnomAD3 genomes

AF:

0.00413

AC:

628

AN:

152152

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00130

Gnomad AMI

AF:

0.00440

Gnomad AMR

AF:

0.00465

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.000192

Gnomad SAS

AF:

0.00249

Gnomad FIN

AF:

0.00132

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.00681

Gnomad OTH

AF:

0.00382

GnomAD3 exomes

AF:

0.00432

AC:

1083

AN:

250580

Hom.:

AF XY:

0.00455

AC XY:

616

AN XY:

135432

show subpopulations

Gnomad AFR exome

AF:

0.00111

Gnomad AMR exome

AF:

0.00363

Gnomad ASJ exome

AF:

0.000199

Gnomad EAS exome

AF:

0.0000544

Gnomad SAS exome

AF:

0.00266

Gnomad FIN exome

AF:

0.00250

Gnomad NFE exome

AF:

0.00685

Gnomad OTH exome

AF:

0.00426

GnomAD4 exome

AF:

0.00603

AC:

8803

AN:

1460562

Hom.:

Cov.:

AF XY:

0.00596

AC XY:

4333

AN XY:

726594

show subpopulations

Gnomad4 AFR exome

AF:

0.000838

Gnomad4 AMR exome

AF:

0.00407

Gnomad4 ASJ exome

AF:

0.000153

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00302

Gnomad4 FIN exome

AF:

0.00253

Gnomad4 NFE exome

AF:

0.00711

Gnomad4 OTH exome

AF:

0.00479

GnomAD4 genome

AF:

0.00412

AC:

627

AN:

152270

Hom.:

Cov.:

AF XY:

0.00367

AC XY:

273

AN XY:

74462

show subpopulations

Gnomad4 AFR

AF:

0.00130

Gnomad4 AMR

AF:

0.00464

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.000193

Gnomad4 SAS

AF:

0.00249

Gnomad4 FIN

AF:

0.00132

Gnomad4 NFE

AF:

0.00681

Gnomad4 OTH

AF:

0.00378

Alfa

AF:

0.00439

Hom.:

Bravo

AF:

0.00428

Asia WGS

AF:

0.00115

AC:

AN:

3476

EpiCase

AF:

0.00606

EpiControl

AF:

0.00616

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jul 31, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.56

CADD

Benign

6.1

DANN

Benign

0.46

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over