chr10-116813010-T-C

Variant names:

• chr10-116813010-T-C
• rs1681748
• NM_001330164.2:c.91+21925A>G

Variant summary

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

Score: -12 - Benign

-12

BP4_StrongBA1

The NM_001330164.2(HSPA12A):​c.91+21925A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.372 in 151,848 control chromosomes in the GnomAD database, including 11,078 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 0.37 (11078 hom., cov: 31)
• Consequence: HSPA12A NM_001330164.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.213
• 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=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.438 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HSPA12A	NM_001330164.2	c.91+21925A>G		intron_variant	Intron 2 of 12		NP_001317093.1
HSPA12A	XM_005269673.6	c.88+21925A>G		intron_variant	Intron 2 of 12		XP_005269730.1
HSPA12A	XM_011539579.3	c.88+21925A>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+21925A>G		intron_variant	Intron 2 of 12	5		ENSP00000489674.1
HSPA12A	ENST00000674197.1	c.88+21925A>G		intron_variant	Intron 2 of 12			ENSP00000501472.1
HSPA12A	ENST00000674167.1	c.-124+21925A>G		intron_variant	Intron 2 of 11			ENSP00000501417.1

Frequencies

GnomAD3 genomes AF: 0.373 AC: 56537 AN: 151730 Hom.: 11081 Cov.: 31

Gnomad AFR AF: 0.278

Gnomad AMI AF: 0.296

Gnomad AMR AF: 0.378

Gnomad ASJ AF: 0.475

Gnomad EAS AF: 0.140

Gnomad SAS AF: 0.329

Gnomad FIN AF: 0.377

Gnomad MID AF: 0.471

Gnomad NFE AF: 0.442

Gnomad OTH AF: 0.421

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

GnomAD4 genome AF: 0.372 AC: 56538 AN: 151848 Hom.: 11078 Cov.: 31 AF XY: 0.369 AC XY: 27376 AN XY: 74182

African (AFR) AF: 0.278 AC: 11512 AN: 41392

American (AMR) AF: 0.378 AC: 5765 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.475 AC: 1648 AN: 3468

East Asian (EAS) AF: 0.139 AC: 717 AN: 5148

South Asian (SAS) AF: 0.329 AC: 1581 AN: 4802

European-Finnish (FIN) AF: 0.377 AC: 3973 AN: 10530

Middle Eastern (MID) AF: 0.486 AC: 142 AN: 292

European-Non Finnish (NFE) AF: 0.442 AC: 30051 AN: 67930

Other (OTH) AF: 0.417 AC: 879 AN: 2108

Alfa AF: 0.402 Hom.: 6525

Bravo AF: 0.365

Asia WGS AF: 0.232 AC: 806 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.4
DANN	Benign	0.51
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs1681748; hg19: chr10-118572521;