dbSNP rs2292152: SGTB:c.*295A>G (chr5-65669951-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_019072.3(SGTB):c.*295A>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 0.0335 in 259,270 control chromosomes in the GnomAD database, including 249 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 0.035 ( 152 hom., cov: 33)

Exomes 𝑓: 0.031 ( 97 hom. )

Consequence

SGTB
NM_019072.3 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.32

Publications

5 publications found

Variant links:

Genes affected

SGTB (HGNC:23567): (small glutamine rich tetratricopeptide repeat co-chaperone beta) Predicted to enable molecular adaptor activity. Predicted to be involved in positive regulation of chaperone-mediated protein folding; posttranslational protein targeting to endoplasmic reticulum membrane; and ubiquitin-dependent ERAD pathway. Predicted to be part of TRC complex. Predicted to be active in membrane. [provided by Alliance of Genome Resources, Apr 2022]

SGTB 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 (BayesDel_noAF=-0.23).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0822 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
SGTB	NM_019072.3 link	c.*295A>G	3_prime_UTR_variant	Exon 11 of 11	ENST00000381007.9	NP_061945.1	Q96EQ0
SGTB	XM_005248548.4 link	c.*295A>G	3_prime_UTR_variant	Exon 11 of 11		XP_005248605.1	Q96EQ0
SGTB	XM_047417334.1 link	c.*295A>G	3_prime_UTR_variant	Exon 10 of 10		XP_047273290.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SGTB	ENST00000381007.9 link	c.*295A>G		3_prime_UTR_variant	Exon 11 of 11	1	NM_019072.3	ENSP00000370395.4		Q96EQ0

Frequencies

GnomAD3 genomes

AF:

0.0349

AC:

5316

AN:

152212

Hom.:

149

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0497

Gnomad AMI

AF:

0.0406

Gnomad AMR

AF:

0.0321

Gnomad ASJ

AF:

0.0637

Gnomad EAS

AF:

0.0864

Gnomad SAS

AF:

0.0897

Gnomad FIN

AF:

0.00160

Gnomad MID

AF:

0.0854

Gnomad NFE

AF:

0.0219

Gnomad OTH

AF:

0.0431

GnomAD4 exome

AF:

0.0313

AC:

3352

AN:

106940

Hom.:

Cov.:

AF XY:

0.0327

AC XY:

1817

AN XY:

55588

show subpopulations

African (AFR)

AF:

0.0546

AC:

179

AN:

3276

American (AMR)

AF:

0.0256

AC:

105

AN:

4098

Ashkenazi Jewish (ASJ)

AF:

0.0678

AC:

257

AN:

3790

East Asian (EAS)

AF:

0.0827

AC:

598

AN:

7228

South Asian (SAS)

AF:

0.0811

AC:

442

AN:

5448

European-Finnish (FIN)

AF:

0.00243

AC:

AN:

6170

Middle Eastern (MID)

AF:

0.0889

AC:

AN:

506

European-Non Finnish (NFE)

AF:

0.0206

AC:

1435

AN:

69572

Other (OTH)

AF:

0.0403

AC:

276

AN:

6852

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.508

Heterozygous variant carriers

156

312

467

623

779

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

110

<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:

0.0350

AC:

5334

AN:

152330

Hom.:

152

Cov.:

AF XY:

0.0357

AC XY:

2660

AN XY:

74512

show subpopulations

African (AFR)

AF:

0.0500

AC:

2076

AN:

41558

American (AMR)

AF:

0.0321

AC:

491

AN:

15304

Ashkenazi Jewish (ASJ)

AF:

0.0637

AC:

221

AN:

3472

East Asian (EAS)

AF:

0.0862

AC:

447

AN:

5186

South Asian (SAS)

AF:

0.0892

AC:

431

AN:

4832

European-Finnish (FIN)

AF:

0.00160

AC:

AN:

10628

Middle Eastern (MID)

AF:

0.0884

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0219

AC:

1491

AN:

68034

Other (OTH)

AF:

0.0460

AC:

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

268

536

805

1073

1341

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

144

216

288

360

<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:

0.0264

Hom.:

Bravo

AF:

0.0367

Asia WGS

AF:

0.117

AC:

406

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.23

CADD

Benign

(source)

DANN

Benign

0.86

PhyloP100

1.3

Mutation Taster

=98/2

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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