5-65669951-T-C

Variant names:

• chr5-65669951-T-C
• rs2292152
• NM_019072.3:c.*295A>G

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_019072.3(SGTB):​c.*295A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0335 in 259,270 control chromosomes in the GnomAD database, including 249 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 0.035 (152 hom., cov: 33)
  • Exomes 𝑓: 0.031 (97 hom.)
• Consequence: SGTB NM_019072.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.32
• Publications: 5 publications found

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

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.23).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0822 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_019072.3. 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
	SGTB	NM_019072.3	MANE Select	c.*295A>G		3_prime_UTR	Exon 11 of 11	NP_061945.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SGTB	ENST00000381007.9	TSL:1 MANE Select	c.*295A>G		3_prime_UTR	Exon 11 of 11	ENSP00000370395.4

Frequencies

GnomAD3 genomes AF: 0.0349 AC: 5316 AN: 152212 Hom.: 149 Cov.: 33

Gnomad AFR AF: 0.0497

Gnomad AMI AF: 0.0406

Gnomad AMR AF: 0.0321

Gnomad ASJ AF: 0.0637

Gnomad EAS AF: 0.0864

Gnomad SAS AF: 0.0897

Gnomad FIN AF: 0.00160

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0219

Gnomad OTH AF: 0.0431

GnomAD4 exome AF: 0.0313 AC: 3352 AN: 106940 Hom.: 97 Cov.: 0 AF XY: 0.0327 AC XY: 1817 AN XY: 55588

African (AFR) AF: 0.0546 AC: 179 AN: 3276

American (AMR) AF: 0.0256 AC: 105 AN: 4098

Ashkenazi Jewish (ASJ) AF: 0.0678 AC: 257 AN: 3790

East Asian (EAS) AF: 0.0827 AC: 598 AN: 7228

South Asian (SAS) AF: 0.0811 AC: 442 AN: 5448

European-Finnish (FIN) AF: 0.00243 AC: 15 AN: 6170

Middle Eastern (MID) AF: 0.0889 AC: 45 AN: 506

European-Non Finnish (NFE) AF: 0.0206 AC: 1435 AN: 69572

Other (OTH) AF: 0.0403 AC: 276 AN: 6852

GnomAD4 genome AF: 0.0350 AC: 5334 AN: 152330 Hom.: 152 Cov.: 33 AF XY: 0.0357 AC XY: 2660 AN XY: 74512

African (AFR) AF: 0.0500 AC: 2076 AN: 41558

American (AMR) AF: 0.0321 AC: 491 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0637 AC: 221 AN: 3472

East Asian (EAS) AF: 0.0862 AC: 447 AN: 5186

South Asian (SAS) AF: 0.0892 AC: 431 AN: 4832

European-Finnish (FIN) AF: 0.00160 AC: 17 AN: 10628

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.0219 AC: 1491 AN: 68034

Other (OTH) AF: 0.0460 AC: 97 AN: 2110

Alfa AF: 0.0264 Hom.: 57

Bravo AF: 0.0367

Asia WGS AF: 0.117 AC: 406 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.23
CADD	Benign	16
DANN	Benign	0.86
PhyloP100		1.3
Mutation Taster		=98/2	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: rs2292152; hg19: chr5-64965778;