rs741103

Variant names:

• chr19-2771643-T-C
• rs741103
• NM_003021.4:c.-23-2552A>G

Variant summary

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

The NM_003021.4(SGTA):​c.-23-2552A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.244 in 149,524 control chromosomes in the GnomAD database, including 5,218 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 0.24 (5218 hom., cov: 31)
• Consequence: SGTA NM_003021.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.407

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=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.527 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SGTA	NM_003021.4	c.-23-2552A>G		intron_variant	Intron 1 of 11	ENST00000221566.7	NP_003012.1
SGTA	XM_011528178.4	c.-23-2552A>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.-23-2552A>G		intron_variant	Intron 1 of 11	1	NM_003021.4	ENSP00000221566.1

Frequencies

GnomAD3 genomes AF: 0.244 AC: 36461 AN: 149414 Hom.: 5203 Cov.: 31

Gnomad AFR AF: 0.360

Gnomad AMI AF: 0.139

Gnomad AMR AF: 0.250

Gnomad ASJ AF: 0.182

Gnomad EAS AF: 0.544

Gnomad SAS AF: 0.252

Gnomad FIN AF: 0.202

Gnomad MID AF: 0.166

Gnomad NFE AF: 0.163

Gnomad OTH AF: 0.223

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

GnomAD4 genome AF: 0.244 AC: 36521 AN: 149524 Hom.: 5218 Cov.: 31 AF XY: 0.251 AC XY: 18272 AN XY: 72796

Gnomad4 AFR AF: 0.360

Gnomad4 AMR AF: 0.250

Gnomad4 ASJ AF: 0.182

Gnomad4 EAS AF: 0.544

Gnomad4 SAS AF: 0.252

Gnomad4 FIN AF: 0.202

Gnomad4 NFE AF: 0.163

Gnomad4 OTH AF: 0.224

Alfa AF: 0.179 Hom.: 3388

Bravo AF: 0.251

Asia WGS AF: 0.390 AC: 1358 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.3
DANN	Benign	0.72

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: rs741103; hg19: chr19-2771641;