ENST00000334701.11:c.367-4028G>T

Variant names:

• chr14-102090406-C-A
• rs11621560
• ENST00000334701.11:c.367-4028G>T

Variant summary

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

The ENST00000334701.11(HSP90AA1):​c.367-4028G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.576 in 151,604 control chromosomes in the GnomAD database, including 26,875 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 0.58 (26875 hom., cov: 30)
• Consequence: HSP90AA1 ENST00000334701.11 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.38

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.764 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HSP90AA1	NM_001017963.3	c.367-4028G>T		intron_variant	Intron 2 of 11		NP_001017963.2
HSP90AA1	XM_011536718.3	c.364-4028G>T		intron_variant	Intron 2 of 11		XP_011535020.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HSP90AA1	ENST00000334701.11	c.367-4028G>T		intron_variant	Intron 2 of 11	1		ENSP00000335153.7
HSP90AA1	ENST00000557234.1	n.156-4028G>T		intron_variant	Intron 1 of 2	3		ENSP00000452241.1

Frequencies

GnomAD3 genomes AF: 0.576 AC: 87245 AN: 151488 Hom.: 26867 Cov.: 30

Gnomad AFR AF: 0.338

Gnomad AMI AF: 0.714

Gnomad AMR AF: 0.695

Gnomad ASJ AF: 0.694

Gnomad EAS AF: 0.784

Gnomad SAS AF: 0.545

Gnomad FIN AF: 0.674

Gnomad MID AF: 0.620

Gnomad NFE AF: 0.656

Gnomad OTH AF: 0.595

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

GnomAD4 genome AF: 0.576 AC: 87265 AN: 151604 Hom.: 26875 Cov.: 30 AF XY: 0.580 AC XY: 42905 AN XY: 74006

Gnomad4 AFR AF: 0.337

Gnomad4 AMR AF: 0.696

Gnomad4 ASJ AF: 0.694

Gnomad4 EAS AF: 0.784

Gnomad4 SAS AF: 0.545

Gnomad4 FIN AF: 0.674

Gnomad4 NFE AF: 0.656

Gnomad4 OTH AF: 0.598

Alfa AF: 0.642 Hom.: 44746

Bravo AF: 0.571

Asia WGS AF: 0.703 AC: 2444 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.12
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11621560; hg19: chr14-102556743;