rs740363

chr10-116816095-G-A

Variant summary

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

The NM_001330164.2(HSPA12A):c.91+18840C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.402 in 152,010 control chromosomes in the GnomAD database, including 13,031 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 0.40 (13031 hom., cov: 32)
• Consequence: HSPA12A NM_001330164.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.241

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 (NFE) allele frequency at 95% confidence interval = 0.478 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HSPA12A	NM_001330164.2	c.91+18840C>T		intron_variant
HSPA12A	XM_005269673.6	c.88+18840C>T		intron_variant
HSPA12A	XM_011539579.3	c.88+18840C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HSPA12A	ENST00000635765.1	c.91+18840C>T		intron_variant		5
HSPA12A	ENST00000674167.1	c.-124+18840C>T		intron_variant
HSPA12A	ENST00000674197.1	c.88+18840C>T		intron_variant

Frequencies

GnomAD3 genomes AF: 0.402 AC: 61090 AN: 151892 Hom.: 13030 Cov.: 32

Gnomad AFR AF: 0.302

Gnomad AMI AF: 0.354

Gnomad AMR AF: 0.407

Gnomad ASJ AF: 0.483

Gnomad EAS AF: 0.132

Gnomad SAS AF: 0.349

Gnomad FIN AF: 0.396

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.482

Gnomad OTH AF: 0.448

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

GnomAD4 genome AF: 0.402 AC: 61106 AN: 152010 Hom.: 13031 Cov.: 32 AF XY: 0.397 AC XY: 29477 AN XY: 74288

Gnomad4 AFR AF: 0.302

Gnomad4 AMR AF: 0.407

Gnomad4 ASJ AF: 0.483

Gnomad4 EAS AF: 0.131

Gnomad4 SAS AF: 0.350

Gnomad4 FIN AF: 0.396

Gnomad4 NFE AF: 0.482

Gnomad4 OTH AF: 0.443

Alfa AF: 0.464 Hom.: 39539

Bravo AF: 0.396

Asia WGS AF: 0.232 AC: 808 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	1.4
Dann	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs740363; hg19: chr10-118575606;