rs6794514

Positions:

• chr3-137880713-T-C
• chr3-137880713-T-G

Variant summary

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

The ENST00000485881.1(HSPA8P9):​n.419T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.855 in 816,798 control chromosomes in the GnomAD database, including 300,103 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 0.85 (55566 hom., cov: 30)
  • Exomes 𝑓: 0.86 (244537 hom.)
• Consequence: HSPA8P9 ENST00000485881.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.53

Genes affected

HSPA8P9 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.63).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.88 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
HSPA8P9		n.137880713T>C		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
HSPA8P9	ENST00000485881.1	n.419T>C		non_coding_transcript_exon_variant	1/1	6

Frequencies

GnomAD3 genomes AF: 0.854 AC: 129742 AN: 151888 Hom.: 55525 Cov.: 30

Gnomad AFR AF: 0.841

Gnomad AMI AF: 0.810

Gnomad AMR AF: 0.791

Gnomad ASJ AF: 0.925

Gnomad EAS AF: 0.730

Gnomad SAS AF: 0.803

Gnomad FIN AF: 0.853

Gnomad MID AF: 0.899

Gnomad NFE AF: 0.886

Gnomad OTH AF: 0.867

GnomAD4 exome AF: 0.855 AC: 568436 AN: 664792 Hom.: 244537 Cov.: 7 AF XY: 0.856 AC XY: 307836 AN XY: 359824

Gnomad4 AFR exome AF: 0.845

Gnomad4 AMR exome AF: 0.691

Gnomad4 ASJ exome AF: 0.925

Gnomad4 EAS exome AF: 0.743

Gnomad4 SAS exome AF: 0.808

Gnomad4 FIN exome AF: 0.853

Gnomad4 NFE exome AF: 0.888

Gnomad4 OTH exome AF: 0.870

GnomAD4 genome AF: 0.854 AC: 129839 AN: 152006 Hom.: 55566 Cov.: 30 AF XY: 0.851 AC XY: 63192 AN XY: 74278

Gnomad4 AFR AF: 0.841

Gnomad4 AMR AF: 0.791

Gnomad4 ASJ AF: 0.925

Gnomad4 EAS AF: 0.730

Gnomad4 SAS AF: 0.805

Gnomad4 FIN AF: 0.853

Gnomad4 NFE AF: 0.886

Gnomad4 OTH AF: 0.863

Alfa AF: 0.873 Hom.: 7215

Bravo AF: 0.848

Asia WGS AF: 0.776 AC: 2700 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.63
CADD	Benign	2.4
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6794514; hg19: chr3-137599555;