chr10-116747388-G-A

Variant names:

• chr10-116747388-G-A
• rs740598
• NM_001330164.2:c.92-40103C>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.92-40103C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.622 in 152,092 control chromosomes in the GnomAD database, including 29,583 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 0.62 (29583 hom., cov: 34)
• Consequence: HSPA12A NM_001330164.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.632
• Publications: 20 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=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.705 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001330164.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HSPA12A	NM_001330164.2		c.92-40103C>T		intron	N/A	NP_001317093.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HSPA12A	ENST00000635765.1	TSL:5	c.92-40103C>T		intron	N/A	ENSP00000489674.1
	HSPA12A	ENST00000674197.1		c.89-40103C>T		intron	N/A	ENSP00000501472.1
	HSPA12A	ENST00000674167.1		c.-123-42110C>T		intron	N/A	ENSP00000501417.1

Frequencies

GnomAD3 genomes AF: 0.622 AC: 94511 AN: 151974 Hom.: 29545 Cov.: 34

Gnomad AFR AF: 0.629

Gnomad AMI AF: 0.701

Gnomad AMR AF: 0.600

Gnomad ASJ AF: 0.478

Gnomad EAS AF: 0.572

Gnomad SAS AF: 0.726

Gnomad FIN AF: 0.678

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.618

Gnomad OTH AF: 0.599

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

GnomAD4 genome AF: 0.622 AC: 94603 AN: 152092 Hom.: 29583 Cov.: 34 AF XY: 0.624 AC XY: 46391 AN XY: 74336

African (AFR) AF: 0.629 AC: 26102 AN: 41510

American (AMR) AF: 0.600 AC: 9171 AN: 15282

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

East Asian (EAS) AF: 0.572 AC: 2946 AN: 5152

South Asian (SAS) AF: 0.725 AC: 3492 AN: 4818

European-Finnish (FIN) AF: 0.678 AC: 7153 AN: 10546

Middle Eastern (MID) AF: 0.520 AC: 153 AN: 294

European-Non Finnish (NFE) AF: 0.618 AC: 42015 AN: 67998

Other (OTH) AF: 0.603 AC: 1272 AN: 2110

Alfa AF: 0.596 Hom.: 11121

Bravo AF: 0.613

Asia WGS AF: 0.669 AC: 2327 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.58
DANN	Benign	0.80
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs740598; hg19: chr10-118506899;