10-116834778-C-T

Variant names:

• chr10-116834778-C-T
• rs2291316
• NM_001330164.2:c.91+157G>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001330164.2(HSPA12A):​c.91+157G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.382 in 152,020 control chromosomes in the GnomAD database, including 12,487 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 (12487 hom., cov: 32)
• Consequence: HSPA12A NM_001330164.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00400

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.487 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HSPA12A	NM_001330164.2	c.91+157G>A		intron_variant	Intron 2 of 12		NP_001317093.1
HSPA12A	XM_005269673.6	c.88+157G>A		intron_variant	Intron 2 of 12		XP_005269730.1
HSPA12A	XM_011539579.3	c.88+157G>A		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+157G>A		intron_variant	Intron 2 of 12	5		ENSP00000489674.1
HSPA12A	ENST00000674197.1	c.88+157G>A		intron_variant	Intron 2 of 12			ENSP00000501472.1
HSPA12A	ENST00000674167.1	c.-124+157G>A		intron_variant	Intron 2 of 11			ENSP00000501417.1

Frequencies

GnomAD3 genomes AF: 0.383 AC: 58136 AN: 151900 Hom.: 12489 Cov.: 32

Gnomad AFR AF: 0.215

Gnomad AMI AF: 0.374

Gnomad AMR AF: 0.393

Gnomad ASJ AF: 0.507

Gnomad EAS AF: 0.135

Gnomad SAS AF: 0.346

Gnomad FIN AF: 0.408

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.492

Gnomad OTH AF: 0.433

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

GnomAD4 genome AF: 0.382 AC: 58136 AN: 152020 Hom.: 12487 Cov.: 32 AF XY: 0.377 AC XY: 28015 AN XY: 74308

Gnomad4 AFR AF: 0.215

Gnomad4 AMR AF: 0.393

Gnomad4 ASJ AF: 0.507

Gnomad4 EAS AF: 0.135

Gnomad4 SAS AF: 0.347

Gnomad4 FIN AF: 0.408

Gnomad4 NFE AF: 0.492

Gnomad4 OTH AF: 0.428

Alfa AF: 0.342 Hom.: 1534

Bravo AF: 0.373

Asia WGS AF: 0.230 AC: 802 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	8.1
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2291316; hg19: chr10-118594289;