rs2238614

chr19-2755341-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.610

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]

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
SGTA	NM_003021.4	c.*599C>T		3_prime_UTR_variant	12/12	ENST00000221566.7
SGTA	XM_011528178.4	c.*599C>T		3_prime_UTR_variant	13/13

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SGTA	ENST00000221566.7	c.*599C>T		3_prime_UTR_variant	12/12	1	NM_003021.4	P1

Frequencies

GnomAD3 genomes AF: 0.219 AC: 33379 AN: 152102 Hom.: 4003 Cov.: 33

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.: 12 AF XY: 0.206 AC XY: 75119 AN XY: 365422

Gnomad4 AFR exome AF: 0.163

Gnomad4 AMR exome AF: 0.258

Gnomad4 ASJ exome AF: 0.252

Gnomad4 EAS exome AF: 0.514

Gnomad4 SAS exome AF: 0.272

Gnomad4 FIN exome AF: 0.212

Gnomad4 NFE exome AF: 0.203

Gnomad4 OTH exome AF: 0.230

GnomAD4 genome AF: 0.219 AC: 33380 AN: 152220 Hom.: 4000 Cov.: 33 AF XY: 0.226 AC XY: 16830 AN XY: 74420

Gnomad4 AFR AF: 0.177

Gnomad4 AMR AF: 0.242

Gnomad4 ASJ AF: 0.255

Gnomad4 EAS AF: 0.510

Gnomad4 SAS AF: 0.283

Gnomad4 FIN AF: 0.191

Gnomad4 NFE AF: 0.214

Gnomad4 OTH AF: 0.224

Alfa AF: 0.217 Hom.: 3724

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
Dann	Benign	0.47
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

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

Other links and lift over

dbSNP: rs2238614; hg19: chr19-2755339; COSMIC: COSV55593527; COSMIC: COSV55593527;