dbSNP rs6053666: SRXN1:c.*468A>G (chr20-648246-T-C) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The NM_080725.3(SRXN1):c.*468A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.364 in 456,294 control chromosomes in the GnomAD database, including 32,013 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 0.39 ( 12364 hom., cov: 32)

Exomes 𝑓: 0.35 ( 19649 hom. )

Consequence

SRXN1
NM_080725.3 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.117

Publications

19 publications found

Variant links:

Genes affected

SRXN1 (HGNC:16132): (sulfiredoxin 1) Enables oxidoreductase activity, acting on a sulfur group of donors. Involved in response to oxidative stress. Located in cytosol. [provided by Alliance of Genome Resources, Apr 2022]

SRXN1 links:

ENSG00000270299 (HGNC:):

ENSG00000270299 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -10 ACMG points.

BP4

Computational evidence support a benign effect (REVEL=0.101).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.535 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SRXN1	NM_080725.3 link	c.*468A>G		3_prime_UTR_variant	Exon 2 of 2	ENST00000381962.4	NP_542763.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SRXN1	ENST00000381962.4 link	c.*468A>G		3_prime_UTR_variant	Exon 2 of 2	1	NM_080725.3	ENSP00000371388.4
ENSG00000270299	ENST00000488788.2 link	c.*610A>G		3_prime_UTR_variant	Exon 3 of 3	2		ENSP00000474279.1

Frequencies

GnomAD3 genomes

AF:

0.389

AC:

59114

AN:

151922

Hom.:

12346

Cov.:

show subpopulations

Gnomad AFR

AF:

0.540

Gnomad AMI

AF:

0.313

Gnomad AMR

AF:

0.275

Gnomad ASJ

AF:

0.364

Gnomad EAS

AF:

0.450

Gnomad SAS

AF:

0.409

Gnomad FIN

AF:

0.370

Gnomad MID

AF:

0.348

Gnomad NFE

AF:

0.323

Gnomad OTH

AF:

0.363

GnomAD2 exomes

AF:

0.352

AC:

45277

AN:

128530

AF XY:

0.356

show subpopulations

Gnomad AFR exome

AF:

0.536

Gnomad AMR exome

AF:

0.248

Gnomad ASJ exome

AF:

0.389

Gnomad EAS exome

AF:

0.452

Gnomad FIN exome

AF:

0.377

Gnomad NFE exome

AF:

0.325

Gnomad OTH exome

AF:

0.339

GnomAD4 exome

AF:

0.351

AC:

106858

AN:

304254

Hom.:

19649

Cov.:

AF XY:

0.357

AC XY:

61826

AN XY:

173210

show subpopulations

African (AFR)

AF:

0.540

AC:

4664

AN:

8644

American (AMR)

AF:

0.250

AC:

6811

AN:

27290

Ashkenazi Jewish (ASJ)

AF:

0.379

AC:

4091

AN:

10804

East Asian (EAS)

AF:

0.456

AC:

4199

AN:

9216

South Asian (SAS)

AF:

0.414

AC:

24732

AN:

59748

European-Finnish (FIN)

AF:

0.367

AC:

4544

AN:

12380

Middle Eastern (MID)

AF:

0.356

AC:

992

AN:

2784

European-Non Finnish (NFE)

AF:

0.325

AC:

51764

AN:

159120

Other (OTH)

AF:

0.355

AC:

5061

AN:

14268

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.510

Heterozygous variant carriers

5767

11534

17301

23068

28835

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

386

772

1158

1544

1930

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.389

AC:

59160

AN:

152040

Hom.:

12364

Cov.:

AF XY:

0.386

AC XY:

28706

AN XY:

74334

show subpopulations

African (AFR)

AF:

0.541

AC:

22422

AN:

41466

American (AMR)

AF:

0.275

AC:

4196

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.364

AC:

1260

AN:

3466

East Asian (EAS)

AF:

0.449

AC:

2321

AN:

5172

South Asian (SAS)

AF:

0.407

AC:

1956

AN:

4810

European-Finnish (FIN)

AF:

0.370

AC:

3919

AN:

10580

Middle Eastern (MID)

AF:

0.361

AC:

106

AN:

294

European-Non Finnish (NFE)

AF:

0.323

AC:

21930

AN:

67944

Other (OTH)

AF:

0.362

AC:

765

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1802

3604

5407

7209

9011

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

566

1132

1698

2264

2830

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.349

Hom.:

22538

Bravo

AF:

0.386

Asia WGS

AF:

0.403

AC:

1401

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

3.5

(source)

DANN

Benign

0.50

PhyloP100

0.12

Mutation Taster

=100/0

polymorphism (auto)

(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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over