19-2778545-G-T

Variant names:

• chr19-2778545-G-T
• rs1005556
• NM_003021.4:c.-24+4688C>A

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+4688C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.371 in 150,994 control chromosomes in the GnomAD database, including 12,878 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 (12878 hom., cov: 30)
• Consequence: SGTA NM_003021.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.02
• Publications: 5 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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.635 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.-24+4688C>A		intron	N/A	NP_003012.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SGTA	ENST00000221566.7	TSL:1 MANE Select	c.-24+4688C>A		intron	N/A	ENSP00000221566.1
	SGTA	ENST00000677562.1		c.-24+4688C>A		intron	N/A	ENSP00000504146.1
	SGTA	ENST00000676943.1		c.-24+4025C>A		intron	N/A	ENSP00000504495.1

Frequencies

GnomAD3 genomes AF: 0.371 AC: 55931 AN: 150876 Hom.: 12849 Cov.: 30

Gnomad AFR AF: 0.631

Gnomad AMI AF: 0.331

Gnomad AMR AF: 0.309

Gnomad ASJ AF: 0.271

Gnomad EAS AF: 0.654

Gnomad SAS AF: 0.448

Gnomad FIN AF: 0.254

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.225

Gnomad OTH AF: 0.346

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

GnomAD4 genome AF: 0.371 AC: 56006 AN: 150994 Hom.: 12878 Cov.: 30 AF XY: 0.379 AC XY: 27949 AN XY: 73752

African (AFR) AF: 0.632 AC: 25926 AN: 41044

American (AMR) AF: 0.309 AC: 4682 AN: 15168

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

East Asian (EAS) AF: 0.654 AC: 3268 AN: 5000

South Asian (SAS) AF: 0.448 AC: 2136 AN: 4772

European-Finnish (FIN) AF: 0.254 AC: 2652 AN: 10424

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

European-Non Finnish (NFE) AF: 0.225 AC: 15287 AN: 67816

Other (OTH) AF: 0.345 AC: 725 AN: 2100

Alfa AF: 0.174 Hom.: 424

Bravo AF: 0.382

Asia WGS AF: 0.562 AC: 1958 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.20
DANN	Benign	0.49
PhyloP100		-2.0
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: rs1005556; hg19: chr19-2778543;