chr10-116728443-C-T

Variant names:

• chr10-116728443-C-T
• rs1665645
• NM_025015.3:c.40+13987G>A

Variant summary

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

The NM_001330164.2(HSPA12A):​c.92-21158G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.692 in 152,114 control chromosomes in the GnomAD database, including 36,922 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 0.69 (36922 hom., cov: 33)
• Consequence: HSPA12A NM_001330164.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.19
• Publications: 3 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=-1.01).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.784 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_025015.3	MANE Select	c.40+13987G>A		intron	N/A	NP_079291.2
	HSPA12A	NM_001330164.2		c.92-21158G>A		intron	N/A	NP_001317093.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HSPA12A	ENST00000369209.8	TSL:1 MANE Select	c.40+13987G>A		intron	N/A	ENSP00000358211.3
	HSPA12A	ENST00000635765.1	TSL:5	c.92-21158G>A		intron	N/A	ENSP00000489674.1
	HSPA12A	ENST00000674197.1		c.89-21158G>A		intron	N/A	ENSP00000501472.1

Frequencies

GnomAD3 genomes AF: 0.692 AC: 105169 AN: 151996 Hom.: 36907 Cov.: 33

Gnomad AFR AF: 0.596

Gnomad AMI AF: 0.644

Gnomad AMR AF: 0.796

Gnomad ASJ AF: 0.845

Gnomad EAS AF: 0.686

Gnomad SAS AF: 0.765

Gnomad FIN AF: 0.603

Gnomad MID AF: 0.867

Gnomad NFE AF: 0.727

Gnomad OTH AF: 0.737

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

GnomAD4 genome AF: 0.692 AC: 105230 AN: 152114 Hom.: 36922 Cov.: 33 AF XY: 0.691 AC XY: 51376 AN XY: 74358

African (AFR) AF: 0.596 AC: 24685 AN: 41452

American (AMR) AF: 0.796 AC: 12181 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.845 AC: 2932 AN: 3470

East Asian (EAS) AF: 0.685 AC: 3550 AN: 5180

South Asian (SAS) AF: 0.765 AC: 3690 AN: 4826

European-Finnish (FIN) AF: 0.603 AC: 6381 AN: 10580

Middle Eastern (MID) AF: 0.871 AC: 256 AN: 294

European-Non Finnish (NFE) AF: 0.727 AC: 49413 AN: 67988

Other (OTH) AF: 0.735 AC: 1556 AN: 2116

Alfa AF: 0.682 Hom.: 5166

Bravo AF: 0.700

Asia WGS AF: 0.719 AC: 2499 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.27
DANN	Benign	0.27
PhyloP100		-1.2
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: rs1665645; hg19: chr10-118487954;