dbSNP rs2238614: SGTA:c.*599C>T (chr19-2755341-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_003021.4(SGTA):c.*599C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.208 in 941,110 control chromosomes in the GnomAD database, including 21,270 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 0.22 ( 4000 hom., cov: 33)

Exomes 𝑓: 0.21 ( 17270 hom. )

Consequence

SGTA
NM_003021.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.610

Publications

17 publications found

Variant links:

Genes affected

SGTA (HGNC:10819): (small glutamine rich tetratricopeptide repeat co-chaperone alpha) This gene encodes a protein which is capable of interacting with the major nonstructural protein of parvovirus H-1 and 70-kDa heat shock cognate protein; however, its function is not known. Since this transcript is expressed ubiquitously in various tissues, this protein may serve a housekeeping function. [provided by RefSeq, Jul 2008]

SGTA links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.88).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.494 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SGTA	NM_003021.4 link	c.*599C>T		3_prime_UTR_variant	Exon 12 of 12	ENST00000221566.7	NP_003012.1
SGTA	XM_011528178.4 link	c.*599C>T		3_prime_UTR_variant	Exon 13 of 13		XP_011526480.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SGTA	ENST00000221566.7 link	c.*599C>T		3_prime_UTR_variant	Exon 12 of 12	1	NM_003021.4	ENSP00000221566.1

Frequencies

GnomAD3 genomes

AF:

0.219

AC:

33379

AN:

152102

Hom.:

4003

Cov.:

show subpopulations

Gnomad AFR

AF:

0.177

Gnomad AMI

AF:

0.342

Gnomad AMR

AF:

0.242

Gnomad ASJ

AF:

0.255

Gnomad EAS

AF:

0.510

Gnomad SAS

AF:

0.283

Gnomad FIN

AF:

0.191

Gnomad MID

AF:

0.247

Gnomad NFE

AF:

0.214

Gnomad OTH

AF:

0.224

GnomAD4 exome

AF:

0.206

AC:

162454

AN:

788890

Hom.:

17270

Cov.:

AF XY:

0.206

AC XY:

75119

AN XY:

365422

show subpopulations

African (AFR)

AF:

0.163

AC:

2443

AN:

14966

American (AMR)

AF:

0.258

AC:

245

AN:

948

Ashkenazi Jewish (ASJ)

AF:

0.252

AC:

1246

AN:

4938

East Asian (EAS)

AF:

0.514

AC:

1750

AN:

3404

South Asian (SAS)

AF:

0.272

AC:

4253

AN:

15638

European-Finnish (FIN)

AF:

0.212

AC:

AN:

264

Middle Eastern (MID)

AF:

0.240

AC:

759

AN:

3168

European-Non Finnish (NFE)

AF:

0.203

AC:

145711

AN:

719560

Other (OTH)

AF:

0.230

AC:

5991

AN:

26004

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

5911

11822

17734

23645

29556

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

7050

14100

21150

28200

35250

<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:

0.219

AC:

33380

AN:

152220

Hom.:

4000

Cov.:

AF XY:

0.226

AC XY:

16830

AN XY:

74420

show subpopulations

African (AFR)

AF:

0.177

AC:

7348

AN:

41552

American (AMR)

AF:

0.242

AC:

3702

AN:

15298

Ashkenazi Jewish (ASJ)

AF:

0.255

AC:

887

AN:

3472

East Asian (EAS)

AF:

0.510

AC:

2633

AN:

5164

South Asian (SAS)

AF:

0.283

AC:

1370

AN:

4834

European-Finnish (FIN)

AF:

0.191

AC:

2028

AN:

10598

Middle Eastern (MID)

AF:

0.238

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.214

AC:

14558

AN:

67984

Other (OTH)

AF:

0.224

AC:

473

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.491

Heterozygous variant carriers

1319

2638

3957

5276

6595

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

356

712

1068

1424

1780

<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:

0.215

Hom.:

4778

Bravo

AF:

0.220

Asia WGS

AF:

0.367

AC:

1277

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

2.2

(source)

DANN

Benign

0.47

PhyloP100

-0.61

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

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