rs1626678

Variant names:

• chr10-116816635-G-A
• rs1626678
• NM_001330164.2:c.91+18300C>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001330164.2(HSPA12A):​c.91+18300C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.4 in 152,006 control chromosomes in the GnomAD database, including 12,955 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 0.40 (12955 hom., cov: 32)
• Consequence: HSPA12A NM_001330164.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0820

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.479 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HSPA12A	NM_001330164.2	c.91+18300C>T		intron_variant	Intron 2 of 12		NP_001317093.1
HSPA12A	XM_005269673.6	c.88+18300C>T		intron_variant	Intron 2 of 12		XP_005269730.1
HSPA12A	XM_011539579.3	c.88+18300C>T		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+18300C>T		intron_variant	Intron 2 of 12	5		ENSP00000489674.1
HSPA12A	ENST00000674197.1	c.88+18300C>T		intron_variant	Intron 2 of 12			ENSP00000501472.1
HSPA12A	ENST00000674167.1	c.-124+18300C>T		intron_variant	Intron 2 of 11			ENSP00000501417.1

Frequencies

GnomAD3 genomes AF: 0.401 AC: 60843 AN: 151886 Hom.: 12954 Cov.: 32

Gnomad AFR AF: 0.294

Gnomad AMI AF: 0.371

Gnomad AMR AF: 0.399

Gnomad ASJ AF: 0.484

Gnomad EAS AF: 0.131

Gnomad SAS AF: 0.347

Gnomad FIN AF: 0.409

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.483

Gnomad OTH AF: 0.444

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

GnomAD4 genome AF: 0.400 AC: 60850 AN: 152006 Hom.: 12955 Cov.: 32 AF XY: 0.395 AC XY: 29332 AN XY: 74298

Gnomad4 AFR AF: 0.293

Gnomad4 AMR AF: 0.399

Gnomad4 ASJ AF: 0.484

Gnomad4 EAS AF: 0.131

Gnomad4 SAS AF: 0.348

Gnomad4 FIN AF: 0.409

Gnomad4 NFE AF: 0.483

Gnomad4 OTH AF: 0.440

Alfa AF: 0.467 Hom.: 22773

Bravo AF: 0.393

Asia WGS AF: 0.230 AC: 800 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.0
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1626678; hg19: chr10-118576146;