rs740595

Positions:

• chr10-116692188-T-C

Variant summary

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

The NM_025015.3(HSPA12A):​c.663+163A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.524 in 152,024 control chromosomes in the GnomAD database, including 21,253 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 (21253 hom., cov: 32)
• Consequence: HSPA12A NM_025015.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.379

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• 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	UniProt
HSPA12A	NM_025015.3	c.663+163A>G		intron_variant		ENST00000369209.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HSPA12A	ENST00000369209.8	c.663+163A>G		intron_variant		1	NM_025015.3	P1

Frequencies

GnomAD3 genomes AF: 0.524 AC: 79525 AN: 151906 Hom.: 21222 Cov.: 32

Gnomad AFR AF: 0.614

Gnomad AMI AF: 0.611

Gnomad AMR AF: 0.473

Gnomad ASJ AF: 0.598

Gnomad EAS AF: 0.332

Gnomad SAS AF: 0.513

Gnomad FIN AF: 0.512

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.491

Gnomad OTH AF: 0.538

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

GnomAD4 genome AF: 0.524 AC: 79600 AN: 152024 Hom.: 21253 Cov.: 32 AF XY: 0.524 AC XY: 38953 AN XY: 74332

Gnomad4 AFR AF: 0.614

Gnomad4 AMR AF: 0.472

Gnomad4 ASJ AF: 0.598

Gnomad4 EAS AF: 0.332

Gnomad4 SAS AF: 0.511

Gnomad4 FIN AF: 0.512

Gnomad4 NFE AF: 0.491

Gnomad4 OTH AF: 0.541

Alfa AF: 0.517 Hom.: 2540

Bravo AF: 0.525

Asia WGS AF: 0.468 AC: 1626 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.7
DANN	Benign	0.47

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: rs740595; hg19: chr10-118451699; COSMIC: COSV65022228;