Variant 14-102083502-A-G details in Genebe, Genetics Data Aggregator

Variant summary

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

The ENST00000216281.13(HSP90AA1):c.1486+44T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.934 in 1,590,332 control chromosomes in the GnomAD database, including 694,067 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 0.92 ( 64808 hom., cov: 31)

Exomes 𝑓: 0.94 ( 629259 hom. )

Consequence

HSP90AA1
ENST00000216281.13 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.470

Variant links:

Genes affected

HSP90AA1 (HGNC:5253): (heat shock protein 90 alpha family class A member 1) The protein encoded by this gene is an inducible molecular chaperone that functions as a homodimer. The encoded protein aids in the proper folding of specific target proteins by use of an ATPase activity that is modulated by co-chaperones. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jan 2012]

HSP90AA1 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=-0.85).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE	Protein
HSP90AA1	NM_005348.4 linkuse as main transcript	c.1486+44T>C	intron_variant	ENST00000216281.13	NP_005339.3
HSP90AA1	NM_001017963.3 linkuse as main transcript	c.1852+44T>C	intron_variant		NP_001017963.2
HSP90AA1	XM_011536718.3 linkuse as main transcript	c.1849+44T>C	intron_variant		XP_011535020.1

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
HSP90AA1	ENST00000216281.13 linkuse as main transcript	c.1486+44T>C	intron_variant		1	NM_005348.4	ENSP00000216281	P1	P07900-1
HSP90AA1	ENST00000334701.11 linkuse as main transcript	c.1852+44T>C	intron_variant		1		ENSP00000335153		P07900-2
HSP90AA1	ENST00000554401.1 linkuse as main transcript	c.*915+44T>C	intron_variant, NMD_transcript_variant		1		ENSP00000451400
HSP90AA1	ENST00000557089.1 linkuse as main transcript	n.634T>C	non_coding_transcript_exon_variant	2/2	2

Frequencies

GnomAD3 genomes

AF:

0.922

AC:

140290

AN:

152140

Hom.:

64760

Cov.:

show subpopulations

Gnomad AFR

AF:

0.888

Gnomad AMI

AF:

0.946

Gnomad AMR

AF:

0.947

Gnomad ASJ

AF:

0.941

Gnomad EAS

AF:

1.00

Gnomad SAS

AF:

0.960

Gnomad FIN

AF:

0.909

Gnomad MID

AF:

0.940

Gnomad NFE

AF:

0.929

Gnomad OTH

AF:

0.919

GnomAD3 exomes

AF:

0.939

AC:

234364

AN:

249496

Hom.:

110218

AF XY:

0.941

AC XY:

127400

AN XY:

135358

show subpopulations

Gnomad AFR exome

AF:

0.883

Gnomad AMR exome

AF:

0.962

Gnomad ASJ exome

AF:

0.936

Gnomad EAS exome

AF:

1.00

Gnomad SAS exome

AF:

0.965

Gnomad FIN exome

AF:

0.915

Gnomad NFE exome

AF:

0.928

Gnomad OTH exome

AF:

0.938

GnomAD4 exome

AF:

0.935

AC:

1344957

AN:

1438074

Hom.:

629259

Cov.:

AF XY:

0.936

AC XY:

671335

AN XY:

717144

show subpopulations

Gnomad4 AFR exome

AF:

0.881

Gnomad4 AMR exome

AF:

0.959

Gnomad4 ASJ exome

AF:

0.937

Gnomad4 EAS exome

AF:

1.00

Gnomad4 SAS exome

AF:

0.962

Gnomad4 FIN exome

AF:

0.913

Gnomad4 NFE exome

AF:

0.932

Gnomad4 OTH exome

AF:

0.938

GnomAD4 genome

AF:

0.922

AC:

140397

AN:

152258

Hom.:

64808

Cov.:

AF XY:

0.923

AC XY:

68728

AN XY:

74434

show subpopulations

Gnomad4 AFR

AF:

0.888

Gnomad4 AMR

AF:

0.947

Gnomad4 ASJ

AF:

0.941

Gnomad4 EAS

AF:

1.00

Gnomad4 SAS

AF:

0.960

Gnomad4 FIN

AF:

0.909

Gnomad4 NFE

AF:

0.929

Gnomad4 OTH

AF:

0.920

Alfa

AF:

0.929

Hom.:

84043

Bravo

AF:

0.923

Asia WGS

AF:

0.973

AC:

3383

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

0.88

DANN

Benign

0.37

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

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

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