Genetic Variant NM_001054.4:c.20T>A (chr16-28595911-A-T) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_001054.4(SULT1A2):c.20T>A(p.Ile7Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 16/22 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 29)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

SULT1A2
NM_001054.4 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.667

Publications

29 publications found

Variant links:

Genes affected

SULT1A2 (HGNC:11454): (sulfotransferase family 1A member 2) 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. This gene encodes one of two phenol sulfotransferases with thermostable enzyme activity. Two alternatively spliced variants that encode the same protein have been described. [provided by RefSeq, Jul 2008]

SULT1A2 links:

ENSG00000288656 (HGNC:):

ENSG00000288656 links:

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (MetaRNN=0.05926597).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001054.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
SULT1A2	NM_001054.4	MANE Select	c.20T>A	p.Ile7Asn	missense	Exon 2 of 8	NP_001045.2	P50226
SULT1A2	NM_001400258.1		c.20T>A	p.Ile7Asn	missense	Exon 3 of 9	NP_001387187.1	P50226
SULT1A2	NM_001400259.1		c.20T>A	p.Ile7Asn	missense	Exon 3 of 9	NP_001387188.1	P50226

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
SULT1A2	ENST00000335715.9	TSL:1 MANE Select	c.20T>A	p.Ile7Asn	missense	Exon 2 of 8	ENSP00000338742.4	P50226
SULT1A2	ENST00000898358.1		c.20T>A	p.Ile7Asn	missense	Exon 2 of 7	ENSP00000568417.1
SULT1A2	ENST00000898343.1		c.20T>A	p.Ile7Asn	missense	Exon 2 of 8	ENSP00000568402.1

Frequencies

GnomAD3 genomes

Cov.:

GnomAD2 exomes

AF:

0.00

AC:

AN:

175472

AF XY:

0.00

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

1380510

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

686794

African (AFR)

AF:

0.00

AC:

AN:

32244

American (AMR)

AF:

0.00

AC:

AN:

41100

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

24980

East Asian (EAS)

AF:

0.00

AC:

AN:

39440

South Asian (SAS)

AF:

0.00

AC:

AN:

83650

European-Finnish (FIN)

AF:

0.00

AC:

AN:

50698

Middle Eastern (MID)

AF:

0.00

AC:

AN:

4018

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

1046862

Other (OTH)

AF:

0.00

AC:

AN:

57518

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.11

BayesDel_addAF

Benign

-0.24

BayesDel_noAF

Benign

-0.58

CADD

Benign

0.019

(source)

DANN

Benign

0.71

DEOGEN2

Benign

0.026

Eigen

Benign

-1.7

Eigen_PC

Benign

-1.8

FATHMM_MKL

Benign

0.025

LIST_S2

Benign

0.014

M_CAP

Benign

0.0030

MetaRNN

Benign

0.059

MetaSVM

Benign

-0.93

MutationAssessor

Benign

1.3

PhyloP100

-0.67

PrimateAI

Benign

0.40

PROVEAN

Benign

-0.78

REVEL

Benign

0.046

Sift

Benign

0.27

Sift4G

Uncertain

0.031

Polyphen

0.070

Vest4

0.15

MutPred

0.48

Gain of disorder (P = 0.0224)

MVP

0.11

MPC

0.13

ClinPred

0.079

GERP RS

-4.5

PromoterAI

-0.0061

Neutral

(source)

Varity_R

0.046

gMVP

0.75

Mutation Taster

=99/1

polymorphism

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over