Variant rs3010460 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The NM_025015.3(HSPA12A):c.835+391G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.377 in 156,930 control chromosomes in the GnomAD database, including 12,183 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 0.38 ( 11887 hom., cov: 32)

Exomes 𝑓: 0.32 ( 296 hom. )

Consequence

HSPA12A
NM_025015.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.77

Variant links:

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 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.38).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.543 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HSPA12A	NM_025015.3 linkuse as main transcript	c.835+391G>C		intron_variant		ENST00000369209.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HSPA12A	ENST00000369209.8 linkuse as main transcript	c.835+391G>C		intron_variant		1	NM_025015.3	P1

Frequencies

GnomAD3 genomes

AF:

0.378

AC:

57437

AN:

151894

Hom.:

11846

Cov.:

show subpopulations

Gnomad AFR

AF:

0.549

Gnomad AMI

AF:

0.241

Gnomad AMR

AF:

0.353

Gnomad ASJ

AF:

0.367

Gnomad EAS

AF:

0.263

Gnomad SAS

AF:

0.224

Gnomad FIN

AF:

0.292

Gnomad MID

AF:

0.385

Gnomad NFE

AF:

0.316

Gnomad OTH

AF:

0.358

GnomAD4 exome

AF:

0.322

AC:

1585

AN:

4918

Hom.:

296

AF XY:

0.313

AC XY:

772

AN XY:

2464

show subpopulations

Gnomad4 AFR exome

AF:

0.547

Gnomad4 AMR exome

AF:

0.291

Gnomad4 ASJ exome

AF:

0.317

Gnomad4 EAS exome

AF:

0.216

Gnomad4 SAS exome

AF:

0.130

Gnomad4 FIN exome

AF:

0.250

Gnomad4 NFE exome

AF:

0.313

Gnomad4 OTH exome

AF:

0.396

GnomAD4 genome

AF:

0.378

AC:

57518

AN:

152012

Hom.:

11887

Cov.:

AF XY:

0.376

AC XY:

27913

AN XY:

74314

show subpopulations

Gnomad4 AFR

AF:

0.549

Gnomad4 AMR

AF:

0.353

Gnomad4 ASJ

AF:

0.367

Gnomad4 EAS

AF:

0.265

Gnomad4 SAS

AF:

0.224

Gnomad4 FIN

AF:

0.292

Gnomad4 NFE

AF:

0.316

Gnomad4 OTH

AF:

0.354

Alfa

AF:

0.233

Hom.:

546

Bravo

AF:

0.391

Asia WGS

AF:

0.263

AC:

914

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.38

CADD

Benign

DANN

Benign

0.73

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over