10-116683400-C-T

Variant names:

• chr10-116683400-C-T
• rs3010460
• NM_025015.3:c.835+391G>A

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_025015.3(HSPA12A):​c.835+391G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: HSPA12A NM_025015.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.77
• Publications: 1 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: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.28).

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.835+391G>A		intron	N/A	NP_079291.2
	HSPA12A	NM_001330164.2		c.886+391G>A		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.835+391G>A		intron	N/A	ENSP00000358211.3	O43301
	HSPA12A	ENST00000635765.1	TSL:5	c.886+391G>A		intron	N/A	ENSP00000489674.1	A0A1B0GTF3
	HSPA12A	ENST00000674197.1		c.883+391G>A		intron	N/A	ENSP00000501472.1	A0A6I8PLB1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 4934 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 2472

African (AFR) AF: 0.00 AC: 0 AN: 254

American (AMR) AF: 0.00 AC: 0 AN: 148

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 208

East Asian (EAS) AF: 0.00 AC: 0 AN: 222

South Asian (SAS) AF: 0.00 AC: 0 AN: 46

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 184

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 22

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 3492

Other (OTH) AF: 0.00 AC: 0 AN: 358

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 546

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.28
CADD	Benign	21
DANN	Benign	0.90
PhyloP100		2.8

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: rs3010460; hg19: chr10-118442911;