rs1665638

Variant names:

• chr10-116738081-T-A
• rs1665638
• NM_025015.3:c.40+4349A>T

Variant summary

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

The NM_025015.3(HSPA12A):​c.40+4349A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0845 in 152,232 control chromosomes in the GnomAD database, including 1,094 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 0.085 (1094 hom., cov: 33)
• Consequence: HSPA12A NM_025015.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.16
• Publications: 1 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=-0.59).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.357 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HSPA12A	NM_025015.3	c.40+4349A>T		intron_variant	Intron 1 of 11	ENST00000369209.8	NP_079291.2
HSPA12A	NM_001330164.2	c.92-30796A>T		intron_variant	Intron 2 of 12		NP_001317093.1
HSPA12A	XM_005269673.6	c.89-30796A>T		intron_variant	Intron 2 of 12		XP_005269730.1
HSPA12A	XM_011539579.3	c.89-30796A>T		intron_variant	Intron 3 of 13		XP_011537881.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HSPA12A	ENST00000369209.8	c.40+4349A>T		intron_variant	Intron 1 of 11	1	NM_025015.3	ENSP00000358211.3

Frequencies

GnomAD3 genomes AF: 0.0844 AC: 12843 AN: 152114 Hom.: 1082 Cov.: 33

Gnomad AFR AF: 0.0553

Gnomad AMI AF: 0.0208

Gnomad AMR AF: 0.233

Gnomad ASJ AF: 0.0683

Gnomad EAS AF: 0.371

Gnomad SAS AF: 0.0739

Gnomad FIN AF: 0.0304

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0577

Gnomad OTH AF: 0.0933

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

GnomAD4 genome AF: 0.0845 AC: 12866 AN: 152232 Hom.: 1094 Cov.: 33 AF XY: 0.0876 AC XY: 6522 AN XY: 74422

African (AFR) AF: 0.0551 AC: 2291 AN: 41568

American (AMR) AF: 0.234 AC: 3584 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0683 AC: 237 AN: 3470

East Asian (EAS) AF: 0.371 AC: 1915 AN: 5158

South Asian (SAS) AF: 0.0746 AC: 359 AN: 4812

European-Finnish (FIN) AF: 0.0304 AC: 323 AN: 10610

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.0577 AC: 3923 AN: 68008

Other (OTH) AF: 0.0928 AC: 196 AN: 2112

Alfa AF: 0.0676 Hom.: 67

Bravo AF: 0.103

Asia WGS AF: 0.219 AC: 760 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.59
CADD	Benign	18
DANN	Benign	0.61
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: rs1665638; hg19: chr10-118497592;