rs1665650

chr10-116727589-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.40+14841A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.692 in 152,002 control chromosomes in the GnomAD database, including 36,910 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 0.69 (36910 hom., cov: 31)
• Consequence: HSPA12A NM_025015.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.302

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=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.784 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HSPA12A	NM_025015.3	c.40+14841A>G		intron_variant		ENST00000369209.8
HSPA12A	NM_001330164.2	c.92-20304A>G		intron_variant
HSPA12A	XM_005269673.6	c.89-20304A>G		intron_variant
HSPA12A	XM_011539579.3	c.89-20304A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HSPA12A	ENST00000369209.8	c.40+14841A>G		intron_variant		1	NM_025015.3	P1

Frequencies

GnomAD3 genomes AF: 0.692 AC: 105106 AN: 151884 Hom.: 36893 Cov.: 31

Gnomad AFR AF: 0.596

Gnomad AMI AF: 0.643

Gnomad AMR AF: 0.796

Gnomad ASJ AF: 0.846

Gnomad EAS AF: 0.686

Gnomad SAS AF: 0.765

Gnomad FIN AF: 0.603

Gnomad MID AF: 0.873

Gnomad NFE AF: 0.727

Gnomad OTH AF: 0.739

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

GnomAD4 genome AF: 0.692 AC: 105169 AN: 152002 Hom.: 36910 Cov.: 31 AF XY: 0.691 AC XY: 51325 AN XY: 74278

Gnomad4 AFR AF: 0.596

Gnomad4 AMR AF: 0.796

Gnomad4 ASJ AF: 0.846

Gnomad4 EAS AF: 0.686

Gnomad4 SAS AF: 0.765

Gnomad4 FIN AF: 0.603

Gnomad4 NFE AF: 0.727

Gnomad4 OTH AF: 0.737

Alfa AF: 0.715 Hom.: 9214

Bravo AF: 0.700

Asia WGS AF: 0.719 AC: 2501 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	3.2
Dann	Benign	0.39

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: rs1665650; hg19: chr10-118487100;