rs10787728

Variant names:

• chr10-116750088-C-T
• rs10787728
• NM_001330164.2:c.92-42803G>A

Variant summary

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

The NM_001330164.2(HSPA12A):​c.92-42803G>A variant causes a intron change. The variant allele was found at a frequency of 0.766 in 387,742 control chromosomes in the GnomAD database, including 118,636 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 0.71 (40921 hom., cov: 32)
  • Exomes 𝑓: 0.80 (77715 hom.)
• Consequence: HSPA12A NM_001330164.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.78

Genes affected

HSPA12A (HGNC:19022): (heat shock protein family A (Hsp70) member 12A) Predicted to enable ATP binding activity. Located in extracellular exosome. [provided by Alliance of Genome Resources, Apr 2022]

RPL5P27 (HGNC:36172): (ribosomal protein L5 pseudogene 27)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.56).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.841 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HSPA12A	NM_001330164.2	c.92-42803G>A		intron_variant	Intron 2 of 12		NP_001317093.1
HSPA12A	XM_005269673.6	c.89-42803G>A		intron_variant	Intron 2 of 12		XP_005269730.1
HSPA12A	XM_011539579.3	c.89-42803G>A		intron_variant	Intron 3 of 13		XP_011537881.1
RPL5P27		n.116750088C>T		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HSPA12A	ENST00000635765.1	c.92-42803G>A		intron_variant	Intron 2 of 12	5		ENSP00000489674.1
HSPA12A	ENST00000674197.1	c.89-42803G>A		intron_variant	Intron 2 of 12			ENSP00000501472.1
HSPA12A	ENST00000674167.1	c.-123-44810G>A		intron_variant	Intron 2 of 11			ENSP00000501417.1

Frequencies

GnomAD3 genomes AF: 0.706 AC: 107275 AN: 151980 Hom.: 40919 Cov.: 32

Gnomad AFR AF: 0.388

Gnomad AMI AF: 0.948

Gnomad AMR AF: 0.748

Gnomad ASJ AF: 0.818

Gnomad EAS AF: 0.610

Gnomad SAS AF: 0.855

Gnomad FIN AF: 0.892

Gnomad MID AF: 0.823

Gnomad NFE AF: 0.847

Gnomad OTH AF: 0.727

GnomAD4 exome AF: 0.804 AC: 189527 AN: 235644 Hom.: 77715 Cov.: 0 AF XY: 0.809 AC XY: 102056 AN XY: 126114

Gnomad4 AFR exome AF: 0.384

Gnomad4 AMR exome AF: 0.754

Gnomad4 ASJ exome AF: 0.831

Gnomad4 EAS exome AF: 0.597

Gnomad4 SAS exome AF: 0.857

Gnomad4 FIN exome AF: 0.881

Gnomad4 NFE exome AF: 0.843

Gnomad4 OTH exome AF: 0.796

GnomAD4 genome AF: 0.705 AC: 107299 AN: 152098 Hom.: 40921 Cov.: 32 AF XY: 0.711 AC XY: 52836 AN XY: 74348

Gnomad4 AFR AF: 0.388

Gnomad4 AMR AF: 0.748

Gnomad4 ASJ AF: 0.818

Gnomad4 EAS AF: 0.609

Gnomad4 SAS AF: 0.855

Gnomad4 FIN AF: 0.892

Gnomad4 NFE AF: 0.847

Gnomad4 OTH AF: 0.727

Alfa AF: 0.807 Hom.: 28577

Bravo AF: 0.674

Asia WGS AF: 0.692 AC: 2406 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.56
CADD	Benign	1.4
DANN	Benign	0.53

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs10787728; hg19: chr10-118509599; COSMIC: COSV70898055;