rs1882881

Positions:

• chr21-14382665-G-T

Variant summary

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

The NM_006948.5(HSPA13):​c.25+430C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.591 in 151,700 control chromosomes in the GnomAD database, including 27,344 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 0.59 (27344 hom., cov: 30)
• Consequence: HSPA13 NM_006948.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.18

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=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.677 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HSPA13	NM_006948.5	c.25+430C>A		intron_variant		ENST00000285667.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HSPA13	ENST00000285667.4	c.25+430C>A		intron_variant		1	NM_006948.5	P1
HSPA13	ENST00000478035.1	n.208+612C>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.591 AC: 89639 AN: 151580 Hom.: 27350 Cov.: 30

Gnomad AFR AF: 0.451

Gnomad AMI AF: 0.691

Gnomad AMR AF: 0.529

Gnomad ASJ AF: 0.700

Gnomad EAS AF: 0.511

Gnomad SAS AF: 0.573

Gnomad FIN AF: 0.645

Gnomad MID AF: 0.674

Gnomad NFE AF: 0.682

Gnomad OTH AF: 0.602

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

GnomAD4 genome AF: 0.591 AC: 89654 AN: 151700 Hom.: 27344 Cov.: 30 AF XY: 0.589 AC XY: 43663 AN XY: 74132

Gnomad4 AFR AF: 0.451

Gnomad4 AMR AF: 0.529

Gnomad4 ASJ AF: 0.700

Gnomad4 EAS AF: 0.510

Gnomad4 SAS AF: 0.573

Gnomad4 FIN AF: 0.645

Gnomad4 NFE AF: 0.682

Gnomad4 OTH AF: 0.602

Alfa AF: 0.661 Hom.: 55135

Bravo AF: 0.573

Asia WGS AF: 0.544 AC: 1893 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.031
DANN	Benign	0.61

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.050		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: rs1882881; hg19: chr21-15754986;