Variant 10-116776981-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.363

Variant links:

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]

HSPA12A links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Protein	UniProt
HSPA12A	NM_001330164.2 linkuse as main transcript	c.91+57954G>A	intron_variant	NP_001317093.1	A0A1B0GTF3B7Z2M8
HSPA12A	XM_005269673.6 linkuse as main transcript	c.88+57954G>A	intron_variant	XP_005269730.1	A0A6I8PLB1
HSPA12A	XM_011539579.3 linkuse as main transcript	c.88+57954G>A	intron_variant	XP_011537881.1	A0A6I8PLB1

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	Protein	UniProt
HSPA12A	ENST00000635765.1 linkuse as main transcript	c.91+57954G>A	intron_variant	5	ENSP00000489674.1	A0A1B0GTF3
HSPA12A	ENST00000674197.1 linkuse as main transcript	c.88+57954G>A	intron_variant		ENSP00000501472.1	A0A6I8PLB1
HSPA12A	ENST00000674167.1 linkuse as main transcript	c.-124+57954G>A	intron_variant		ENSP00000501417.1	A0A6I8PIT5

Frequencies

GnomAD3 genomes

AF:

0.392

AC:

59532

AN:

152020

Hom.:

12541

Cov.:

show subpopulations

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.:

AF XY:

0.397

AC XY:

29500

AN XY:

74378

show subpopulations

Gnomad4 AFR

AF:

0.236

Gnomad4 AMR

AF:

0.444

Gnomad4 ASJ

AF:

0.486

Gnomad4 EAS

AF:

0.368

Gnomad4 SAS

AF:

0.409

Gnomad4 FIN

AF:

0.484

Gnomad4 NFE

AF:

0.452

Gnomad4 OTH

AF:

0.391

Alfa

AF:

0.442

Hom.:

25166

Bravo

AF:

0.383

Asia WGS

AF:

0.378

AC:

1316

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

1.2

DANN

Benign

0.50

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over