rs3010460

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr10-116683400-C-G
• chr10-116683400-C-T

Variant summary

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

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
• 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: Benign. The variant received -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 rank	MANE	Protein	UniProt
HSPA12A	NM_025015.3	c.835+391G>C		intron_variant	Intron 7 of 11	ENST00000369209.8	NP_079291.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HSPA12A	ENST00000369209.8	c.835+391G>C		intron_variant	Intron 7 of 11	1	NM_025015.3	ENSP00000358211.3

Frequencies

GnomAD3 genomes AF: 0.378 AC: 57437 AN: 151894 Hom.: 11846 Cov.: 32

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

African (AFR) AF: 0.547 AC: 139 AN: 254

American (AMR) AF: 0.291 AC: 43 AN: 148

Ashkenazi Jewish (ASJ) AF: 0.317 AC: 66 AN: 208

East Asian (EAS) AF: 0.216 AC: 48 AN: 222

South Asian (SAS) AF: 0.130 AC: 6 AN: 46

European-Finnish (FIN) AF: 0.250 AC: 46 AN: 184

Middle Eastern (MID) AF: 0.273 AC: 6 AN: 22

European-Non Finnish (NFE) AF: 0.313 AC: 1090 AN: 3478

Other (OTH) AF: 0.396 AC: 141 AN: 356

GnomAD4 genome AF: 0.378 AC: 57518 AN: 152012 Hom.: 11887 Cov.: 32 AF XY: 0.376 AC XY: 27913 AN XY: 74314

African (AFR) AF: 0.549 AC: 22750 AN: 41418

American (AMR) AF: 0.353 AC: 5395 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.367 AC: 1272 AN: 3470

East Asian (EAS) AF: 0.265 AC: 1367 AN: 5160

South Asian (SAS) AF: 0.224 AC: 1077 AN: 4816

European-Finnish (FIN) AF: 0.292 AC: 3088 AN: 10566

Middle Eastern (MID) AF: 0.390 AC: 114 AN: 292

European-Non Finnish (NFE) AF: 0.316 AC: 21489 AN: 67974

Other (OTH) AF: 0.354 AC: 746 AN: 2110

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	20
DANN	Benign	0.73
PhyloP100		2.8
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: rs3010460; hg19: chr10-118442911;