NM_001330164.2:c.91+57954G>A

Variant names:

• chr10-116776981-C-T
• rs1900501
• NM_001330164.2:c.91+57954G>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.91+57954G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.391 in 152,136 control chromosomes in the GnomAD database, including 12,543 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 0.39 (12543 hom., cov: 33)
• Consequence: HSPA12A NM_001330164.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.363
• 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=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.448 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.91+57954G>A		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.91+57954G>A		intron	N/A	ENSP00000489674.1
	HSPA12A	ENST00000674197.1		c.88+57954G>A		intron	N/A	ENSP00000501472.1
	HSPA12A	ENST00000674167.1		c.-124+57954G>A		intron	N/A	ENSP00000501417.1

Frequencies

GnomAD3 genomes AF: 0.392 AC: 59532 AN: 152020 Hom.: 12541 Cov.: 33

Gnomad AFR AF: 0.236

Gnomad AMI AF: 0.667

Gnomad AMR AF: 0.443

Gnomad ASJ AF: 0.486

Gnomad EAS AF: 0.369

Gnomad SAS AF: 0.408

Gnomad FIN AF: 0.484

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.452

Gnomad OTH AF: 0.392

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

GnomAD4 genome AF: 0.391 AC: 59552 AN: 152136 Hom.: 12543 Cov.: 33 AF XY: 0.397 AC XY: 29500 AN XY: 74378

African (AFR) AF: 0.236 AC: 9800 AN: 41526

American (AMR) AF: 0.444 AC: 6793 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.486 AC: 1689 AN: 3472

East Asian (EAS) AF: 0.368 AC: 1905 AN: 5172

South Asian (SAS) AF: 0.409 AC: 1970 AN: 4818

European-Finnish (FIN) AF: 0.484 AC: 5115 AN: 10566

Middle Eastern (MID) AF: 0.446 AC: 131 AN: 294

European-Non Finnish (NFE) AF: 0.452 AC: 30718 AN: 67964

Other (OTH) AF: 0.391 AC: 823 AN: 2106

Alfa AF: 0.433 Hom.: 55985

Bravo AF: 0.383

Asia WGS AF: 0.378 AC: 1316 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	1.2
DANN	Benign	0.50
PhyloP100		-0.36

Splicing

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

Other links and lift over

dbSNP: rs1900501; hg19: chr10-118536492;