rs12479

chr21-14372948-T-Cchr21-14372948-T-A

Variant summary

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

The NM_006948.5(HSPA13):c.*669A>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 0.756 in 152,112 control chromosomes in the GnomAD database, including 43,995 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 0.76 (43994 hom., cov: 33)
  • Exomes 𝑓: 1.0 (1 hom.)
• Consequence: HSPA13 NM_006948.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.247

Genes affected

HSPA13 (HGNC:11375): (heat shock protein family A (Hsp70) member 13) The protein encoded by this gene is a member of the heat shock protein 70 family and is found associated with microsomes. Members of this protein family play a role in the processing of cytosolic and secretory proteins, as well as in the removal of denatured or incorrectly-folded proteins. The encoded protein contains an ATPase domain and has been shown to associate with a ubiquitin-like protein. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.829 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HSPA13	NM_006948.5	c.*669A>G		3_prime_UTR_variant	5/5	ENST00000285667.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HSPA13	ENST00000285667.4	c.*669A>G		3_prime_UTR_variant	5/5	1	NM_006948.5	P1

Frequencies

GnomAD3 genomes AF: 0.756 AC: 114982 AN: 151992 Hom.: 43957 Cov.: 33

Gnomad AFR AF: 0.836

Gnomad AMI AF: 0.768

Gnomad AMR AF: 0.638

Gnomad ASJ AF: 0.793

Gnomad EAS AF: 0.620

Gnomad SAS AF: 0.684

Gnomad FIN AF: 0.733

Gnomad MID AF: 0.848

Gnomad NFE AF: 0.752

Gnomad OTH AF: 0.748

GnomAD4 exome AF: 1.00 AC: 2 AN: 2 Hom.: 1 Cov.: 0 AC XY: 0 AN XY: 0

Gnomad4 NFE exome AF: 1.00

GnomAD4 genome AF: 0.756 AC: 115068 AN: 152110 Hom.: 43994 Cov.: 33 AF XY: 0.753 AC XY: 55975 AN XY: 74370

Gnomad4 AFR AF: 0.836

Gnomad4 AMR AF: 0.637

Gnomad4 ASJ AF: 0.793

Gnomad4 EAS AF: 0.619

Gnomad4 SAS AF: 0.685

Gnomad4 FIN AF: 0.733

Gnomad4 NFE AF: 0.752

Gnomad4 OTH AF: 0.748

Alfa AF: 0.748 Hom.: 72070

Bravo AF: 0.749

Asia WGS AF: 0.660 AC: 2294 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	1.5
Dann	Benign	0.81
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

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: rs12479; hg19: chr21-15745269;