19-2755341-G-A

Variant names:

• chr19-2755341-G-A
• rs2238614
• NM_003021.4:c.*599C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 17 publications found

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

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003021.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SGTA	NM_003021.4	MANE Select	c.*599C>T		3_prime_UTR	Exon 12 of 12	NP_003012.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SGTA	ENST00000221566.7	TSL:1 MANE Select	c.*599C>T		3_prime_UTR	Exon 12 of 12	ENSP00000221566.1
	SGTA	ENST00000676611.1		n.2245C>T		non_coding_transcript_exon	Exon 3 of 3
	SGTA	ENST00000677513.1		n.1971C>T		non_coding_transcript_exon	Exon 11 of 11

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

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: 56 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

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

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: 70 AN: 294

European-Non Finnish (NFE) AF: 0.214 AC: 14558 AN: 67984

Other (OTH) AF: 0.224 AC: 473 AN: 2114

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.2
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)

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

Other links and lift over

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