rs1640262

Variant names:

• chr19-2779136-T-C
• rs1640262
• NM_003021.4:c.-24+4097A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_003021.4(SGTA):​c.-24+4097A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.372 in 152,044 control chromosomes in the GnomAD database, including 13,013 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 0.37 (13013 hom., cov: 32)
• Consequence: SGTA NM_003021.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04
• Publications: 15 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=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.638 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SGTA	NM_003021.4	c.-24+4097A>G		intron_variant	Intron 1 of 11	ENST00000221566.7	NP_003012.1
SGTA	XM_011528178.4	c.-24+3434A>G		intron_variant	Intron 2 of 12		XP_011526480.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SGTA	ENST00000221566.7	c.-24+4097A>G		intron_variant	Intron 1 of 11	1	NM_003021.4	ENSP00000221566.1

Frequencies

GnomAD3 genomes AF: 0.372 AC: 56538 AN: 151926 Hom.: 12989 Cov.: 32

Gnomad AFR AF: 0.631

Gnomad AMI AF: 0.335

Gnomad AMR AF: 0.310

Gnomad ASJ AF: 0.271

Gnomad EAS AF: 0.657

Gnomad SAS AF: 0.453

Gnomad FIN AF: 0.256

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.226

Gnomad OTH AF: 0.343

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.372 AC: 56605 AN: 152044 Hom.: 13013 Cov.: 32 AF XY: 0.381 AC XY: 28279 AN XY: 74318

African (AFR) AF: 0.631 AC: 26161 AN: 41460

American (AMR) AF: 0.310 AC: 4727 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.271 AC: 941 AN: 3468

East Asian (EAS) AF: 0.657 AC: 3386 AN: 5156

South Asian (SAS) AF: 0.452 AC: 2180 AN: 4822

European-Finnish (FIN) AF: 0.256 AC: 2704 AN: 10554

Middle Eastern (MID) AF: 0.299 AC: 88 AN: 294

European-Non Finnish (NFE) AF: 0.226 AC: 15388 AN: 67992

Other (OTH) AF: 0.343 AC: 725 AN: 2116

Alfa AF: 0.279 Hom.: 19425

Bravo AF: 0.382

Asia WGS AF: 0.563 AC: 1959 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.11
DANN	Benign	0.52
PhyloP100		-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: rs1640262; hg19: chr19-2779134;