NM_025015.3:c.41-5919A>G

Variant names:

• chr10-116713204-T-C
• rs4752003
• NM_025015.3:c.41-5919A>G

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_025015.3(HSPA12A):​c.41-5919A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.268 in 150,718 control chromosomes in the GnomAD database, including 5,656 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 0.27 (5656 hom., cov: 29)
• Consequence: HSPA12A NM_025015.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.45
• Publications: 6 publications found

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

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.44).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.411 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_025015.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HSPA12A	NM_025015.3	MANE Select	c.41-5919A>G		intron	N/A	NP_079291.2
	HSPA12A	NM_001330164.2		c.92-5919A>G		intron	N/A	NP_001317093.1	A0A1B0GTF3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HSPA12A	ENST00000369209.8	TSL:1 MANE Select	c.41-5919A>G		intron	N/A	ENSP00000358211.3	O43301
	HSPA12A	ENST00000635765.1	TSL:5	c.92-5919A>G		intron	N/A	ENSP00000489674.1	A0A1B0GTF3
	HSPA12A	ENST00000674197.1		c.89-5919A>G		intron	N/A	ENSP00000501472.1	A0A6I8PLB1

Frequencies

GnomAD3 genomes AF: 0.268 AC: 40317 AN: 150610 Hom.: 5652 Cov.: 29

Gnomad AFR AF: 0.318

Gnomad AMI AF: 0.198

Gnomad AMR AF: 0.261

Gnomad ASJ AF: 0.132

Gnomad EAS AF: 0.426

Gnomad SAS AF: 0.179

Gnomad FIN AF: 0.330

Gnomad MID AF: 0.105

Gnomad NFE AF: 0.233

Gnomad OTH AF: 0.237

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

GnomAD4 genome AF: 0.268 AC: 40340 AN: 150718 Hom.: 5656 Cov.: 29 AF XY: 0.269 AC XY: 19775 AN XY: 73534

African (AFR) AF: 0.317 AC: 13010 AN: 40996

American (AMR) AF: 0.262 AC: 3967 AN: 15162

Ashkenazi Jewish (ASJ) AF: 0.132 AC: 459 AN: 3470

East Asian (EAS) AF: 0.426 AC: 2150 AN: 5050

South Asian (SAS) AF: 0.179 AC: 855 AN: 4774

European-Finnish (FIN) AF: 0.330 AC: 3388 AN: 10280

Middle Eastern (MID) AF: 0.103 AC: 30 AN: 292

European-Non Finnish (NFE) AF: 0.234 AC: 15807 AN: 67694

Other (OTH) AF: 0.236 AC: 493 AN: 2088

Alfa AF: 0.242 Hom.: 15761

Bravo AF: 0.272

Asia WGS AF: 0.278 AC: 966 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.44
CADD	Benign	20
DANN	Benign	0.75
PhyloP100		1.5
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs4752003; hg19: chr10-118472715;