chr14-64543642-C-G

Variant names:

• chr14-64543642-C-G
• rs11848114
• ENST00000394709.2:c.*873C>G

Variant summary

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

The ENST00000394709.2(HSPA2):​c.*873C>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 0.636 in 152,102 control chromosomes in the GnomAD database, including 32,170 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 0.64 (32169 hom., cov: 33)
  • Exomes 𝑓: 1.0 (1 hom.)
• Consequence: HSPA2 ENST00000394709.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.08

Genes affected

HSPA2 (HGNC:5235): (heat shock protein family A (Hsp70) member 2) Enables disordered domain specific binding activity; enzyme binding activity; and unfolded protein binding activity. Involved in negative regulation of inclusion body assembly and protein refolding. Located in cytosol. [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=-0.71).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.868 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HSPA2	ENST00000394709.2	c.*873C>G		3_prime_UTR_variant	Exon 2 of 2	1		ENSP00000378199.1

Frequencies

GnomAD3 genomes AF: 0.636 AC: 96709 AN: 151982 Hom.: 32157 Cov.: 33

Gnomad AFR AF: 0.437

Gnomad AMI AF: 0.737

Gnomad AMR AF: 0.706

Gnomad ASJ AF: 0.656

Gnomad EAS AF: 0.890

Gnomad SAS AF: 0.714

Gnomad FIN AF: 0.835

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.684

Gnomad OTH AF: 0.638

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

Gnomad4 FIN exome AF: 1.00

GnomAD4 genome AF: 0.636 AC: 96744 AN: 152100 Hom.: 32169 Cov.: 33 AF XY: 0.647 AC XY: 48137 AN XY: 74354

Gnomad4 AFR AF: 0.436

Gnomad4 AMR AF: 0.706

Gnomad4 ASJ AF: 0.656

Gnomad4 EAS AF: 0.890

Gnomad4 SAS AF: 0.713

Gnomad4 FIN AF: 0.835

Gnomad4 NFE AF: 0.684

Gnomad4 OTH AF: 0.640

Alfa AF: 0.652 Hom.: 4104

Bravo AF: 0.617

Asia WGS AF: 0.728 AC: 2534 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	12
DANN	Benign	0.61

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: rs11848114; hg19: chr14-65010360;