10-116692533-G-T

Position:

• chr10-116692533-G-T

Variant summary

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

The NM_025015.3(HSPA12A):​c.547-66C>A variant causes a intron change. The variant allele was found at a frequency of 0.498 in 1,262,098 control chromosomes in the GnomAD database, including 158,194 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 0.52 (21342 hom., cov: 33)
  • Exomes 𝑓: 0.49 (136852 hom.)
• Consequence: HSPA12A NM_025015.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.03

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]

HSPA12A (HGNC:):

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 = 0.608 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
HSPA12A	NM_025015.3	c.547-66C>A		intron_variant		ENST00000369209.8	NP_079291.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
HSPA12A	ENST00000369209.8	c.547-66C>A		intron_variant		1	NM_025015.3	ENSP00000358211.3

Frequencies

GnomAD3 genomes AF: 0.525 AC: 79740 AN: 151938 Hom.: 21310 Cov.: 33

Gnomad AFR AF: 0.614

Gnomad AMI AF: 0.612

Gnomad AMR AF: 0.473

Gnomad ASJ AF: 0.597

Gnomad EAS AF: 0.333

Gnomad SAS AF: 0.505

Gnomad FIN AF: 0.512

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.494

Gnomad OTH AF: 0.541

GnomAD4 exome AF: 0.494 AC: 548626 AN: 1110040 Hom.: 136852 AF XY: 0.495 AC XY: 279711 AN XY: 564734

Gnomad4 AFR exome AF: 0.615

Gnomad4 AMR exome AF: 0.483

Gnomad4 ASJ exome AF: 0.609

Gnomad4 EAS exome AF: 0.339

Gnomad4 SAS exome AF: 0.515

Gnomad4 FIN exome AF: 0.514

Gnomad4 NFE exome AF: 0.490

Gnomad4 OTH exome AF: 0.511

GnomAD4 genome AF: 0.525 AC: 79815 AN: 152058 Hom.: 21342 Cov.: 33 AF XY: 0.525 AC XY: 39014 AN XY: 74322

Gnomad4 AFR AF: 0.615

Gnomad4 AMR AF: 0.473

Gnomad4 ASJ AF: 0.597

Gnomad4 EAS AF: 0.333

Gnomad4 SAS AF: 0.502

Gnomad4 FIN AF: 0.512

Gnomad4 NFE AF: 0.494

Gnomad4 OTH AF: 0.544

Alfa AF: 0.520 Hom.: 2573

Bravo AF: 0.526

Asia WGS AF: 0.463 AC: 1611 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	9.4
DANN	Benign	0.68

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: rs2240711; hg19: chr10-118452044; COSMIC: COSV65022326; COSMIC: COSV65022326;