chr5-65670922-A-G

Position:

• chr5-65670922-A-G

Variant summary

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

The NM_019072.3(SGTB):​c.804-565T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.619 in 152,032 control chromosomes in the GnomAD database, including 29,468 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 0.62 (29468 hom., cov: 32)
• Consequence: SGTB NM_019072.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.515

Genes affected

SGTB (HGNC:23567): (small glutamine rich tetratricopeptide repeat co-chaperone beta) Predicted to enable molecular adaptor activity. Predicted to be involved in positive regulation of chaperone-mediated protein folding; posttranslational protein targeting to endoplasmic reticulum membrane; and ubiquitin-dependent ERAD pathway. Predicted to be part of TRC complex. Predicted to be active in membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.638 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SGTB	NM_019072.3	c.804-565T>C		intron_variant		ENST00000381007.9	NP_061945.1
SGTB	XM_005248548.4	c.804-565T>C		intron_variant			XP_005248605.1
SGTB	XM_047417334.1	c.609-565T>C		intron_variant			XP_047273290.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SGTB	ENST00000381007.9	c.804-565T>C		intron_variant		1	NM_019072.3	ENSP00000370395.4

Frequencies

GnomAD3 genomes AF: 0.619 AC: 94092 AN: 151914 Hom.: 29444 Cov.: 32

Gnomad AFR AF: 0.631

Gnomad AMI AF: 0.673

Gnomad AMR AF: 0.540

Gnomad ASJ AF: 0.577

Gnomad EAS AF: 0.433

Gnomad SAS AF: 0.639

Gnomad FIN AF: 0.638

Gnomad MID AF: 0.548

Gnomad NFE AF: 0.643

Gnomad OTH AF: 0.589

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

GnomAD4 genome AF: 0.619 AC: 94154 AN: 152032 Hom.: 29468 Cov.: 32 AF XY: 0.614 AC XY: 45631 AN XY: 74300

Gnomad4 AFR AF: 0.631

Gnomad4 AMR AF: 0.539

Gnomad4 ASJ AF: 0.577

Gnomad4 EAS AF: 0.432

Gnomad4 SAS AF: 0.640

Gnomad4 FIN AF: 0.638

Gnomad4 NFE AF: 0.643

Gnomad4 OTH AF: 0.586

Alfa AF: 0.629 Hom.: 3777

Bravo AF: 0.610

Asia WGS AF: 0.559 AC: 1944 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.1
DANN	Benign	0.53

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: rs27136; hg19: chr5-64966749;