NM_001330164.2:c.92-39959C>T

Variant names:

• chr10-116747244-G-A
• rs740599
• NM_001330164.2:c.92-39959C>T

Variant summary

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

The NM_001330164.2(HSPA12A):​c.92-39959C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.604 in 152,056 control chromosomes in the GnomAD database, including 27,882 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 0.60 (27882 hom., cov: 34)
• Consequence: HSPA12A NM_001330164.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.743
• Publications: 9 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=-0.79).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.704 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HSPA12A	NM_001330164.2	c.92-39959C>T		intron_variant	Intron 2 of 12		NP_001317093.1
HSPA12A	XM_005269673.6	c.89-39959C>T		intron_variant	Intron 2 of 12		XP_005269730.1
HSPA12A	XM_011539579.3	c.89-39959C>T		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.92-39959C>T		intron_variant	Intron 2 of 12	5		ENSP00000489674.1
HSPA12A	ENST00000674197.1	c.89-39959C>T		intron_variant	Intron 2 of 12			ENSP00000501472.1
HSPA12A	ENST00000674167.1	c.-123-41966C>T		intron_variant	Intron 2 of 11			ENSP00000501417.1

Frequencies

GnomAD3 genomes AF: 0.604 AC: 91717 AN: 151938 Hom.: 27851 Cov.: 34

Gnomad AFR AF: 0.565

Gnomad AMI AF: 0.701

Gnomad AMR AF: 0.594

Gnomad ASJ AF: 0.478

Gnomad EAS AF: 0.569

Gnomad SAS AF: 0.724

Gnomad FIN AF: 0.678

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.618

Gnomad OTH AF: 0.588

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

GnomAD4 genome AF: 0.604 AC: 91802 AN: 152056 Hom.: 27882 Cov.: 34 AF XY: 0.606 AC XY: 45003 AN XY: 74304

African (AFR) AF: 0.565 AC: 23449 AN: 41468

American (AMR) AF: 0.595 AC: 9090 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.478 AC: 1660 AN: 3470

East Asian (EAS) AF: 0.569 AC: 2937 AN: 5162

South Asian (SAS) AF: 0.724 AC: 3482 AN: 4812

European-Finnish (FIN) AF: 0.678 AC: 7156 AN: 10562

Middle Eastern (MID) AF: 0.517 AC: 152 AN: 294

European-Non Finnish (NFE) AF: 0.618 AC: 41988 AN: 67978

Other (OTH) AF: 0.593 AC: 1253 AN: 2114

Alfa AF: 0.607 Hom.: 70414

Bravo AF: 0.592

Asia WGS AF: 0.661 AC: 2302 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	16
DANN	Benign	0.52
PhyloP100		0.74

Splicing

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

Other links and lift over

dbSNP: rs740599; hg19: chr10-118506755;