10-116776588-T-C

Variant names:

• chr10-116776588-T-C
• rs10490911
• NM_001330164.2:c.91+58347A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001330164.2(HSPA12A):​c.91+58347A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.019 in 152,290 control chromosomes in the GnomAD database, including 60 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 0.019 (60 hom., cov: 33)
• Consequence: HSPA12A NM_001330164.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.470
• Publications: 0 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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.112 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HSPA12A	NM_001330164.2	c.91+58347A>G		intron_variant	Intron 2 of 12		NP_001317093.1
HSPA12A	XM_005269673.6	c.88+58347A>G		intron_variant	Intron 2 of 12		XP_005269730.1
HSPA12A	XM_011539579.3	c.88+58347A>G		intron_variant	Intron 3 of 13		XP_011537881.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HSPA12A	ENST00000635765.1	c.91+58347A>G		intron_variant	Intron 2 of 12	5		ENSP00000489674.1
HSPA12A	ENST00000674197.1	c.88+58347A>G		intron_variant	Intron 2 of 12			ENSP00000501472.1
HSPA12A	ENST00000674167.1	c.-124+58347A>G		intron_variant	Intron 2 of 11			ENSP00000501417.1

Frequencies

GnomAD3 genomes AF: 0.0189 AC: 2873 AN: 152172 Hom.: 59 Cov.: 33

Gnomad AFR AF: 0.0216

Gnomad AMI AF: 0.00768

Gnomad AMR AF: 0.0102

Gnomad ASJ AF: 0.0112

Gnomad EAS AF: 0.119

Gnomad SAS AF: 0.00932

Gnomad FIN AF: 0.0378

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.00989

Gnomad OTH AF: 0.0163

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

GnomAD4 genome AF: 0.0190 AC: 2887 AN: 152290 Hom.: 60 Cov.: 33 AF XY: 0.0205 AC XY: 1527 AN XY: 74452

African (AFR) AF: 0.0216 AC: 897 AN: 41552

American (AMR) AF: 0.0102 AC: 156 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0112 AC: 39 AN: 3472

East Asian (EAS) AF: 0.120 AC: 621 AN: 5182

South Asian (SAS) AF: 0.00933 AC: 45 AN: 4822

European-Finnish (FIN) AF: 0.0378 AC: 401 AN: 10610

Middle Eastern (MID) AF: 0.0136 AC: 4 AN: 294

European-Non Finnish (NFE) AF: 0.00989 AC: 673 AN: 68030

Other (OTH) AF: 0.0208 AC: 44 AN: 2112

Alfa AF: 0.0133 Hom.: 1

Bravo AF: 0.0182

Asia WGS AF: 0.0710 AC: 246 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	5.3
DANN	Benign	0.31
PhyloP100		0.47

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs10490911; hg19: chr10-118536099;