rs740598

chr10-116747388-G-Achr10-116747388-G-C

Variant summary

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

The NM_001330164.2(HSPA12A):c.92-40103C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.622 in 152,092 control chromosomes in the GnomAD database, including 29,583 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 0.62 (29583 hom., cov: 34)
• Consequence: HSPA12A NM_001330164.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.632

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=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.705 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HSPA12A	NM_001330164.2	c.92-40103C>T		intron_variant
HSPA12A	XM_005269673.6	c.89-40103C>T		intron_variant
HSPA12A	XM_011539579.3	c.89-40103C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HSPA12A	ENST00000635765.1	c.92-40103C>T		intron_variant		5
HSPA12A	ENST00000674167.1	c.-123-42110C>T		intron_variant
HSPA12A	ENST00000674197.1	c.89-40103C>T		intron_variant

Frequencies

GnomAD3 genomes AF: 0.622 AC: 94511 AN: 151974 Hom.: 29545 Cov.: 34

Gnomad AFR AF: 0.629

Gnomad AMI AF: 0.701

Gnomad AMR AF: 0.600

Gnomad ASJ AF: 0.478

Gnomad EAS AF: 0.572

Gnomad SAS AF: 0.726

Gnomad FIN AF: 0.678

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.618

Gnomad OTH AF: 0.599

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

GnomAD4 genome AF: 0.622 AC: 94603 AN: 152092 Hom.: 29583 Cov.: 34 AF XY: 0.624 AC XY: 46391 AN XY: 74336

Gnomad4 AFR AF: 0.629

Gnomad4 AMR AF: 0.600

Gnomad4 ASJ AF: 0.478

Gnomad4 EAS AF: 0.572

Gnomad4 SAS AF: 0.725

Gnomad4 FIN AF: 0.678

Gnomad4 NFE AF: 0.618

Gnomad4 OTH AF: 0.603

Alfa AF: 0.552 Hom.: 3245

Bravo AF: 0.613

Asia WGS AF: 0.669 AC: 2327 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	0.58
Dann	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs740598; hg19: chr10-118506899;