rs17840762

chr9-125241708-G-A

Variant summary

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

The ENST00000468244.2(HSPA5-DT):n.46G>A 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 0.108 in 158,532 control chromosomes in the GnomAD database, including 1,138 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 0.11 (1106 hom., cov: 32)
  • Exomes 𝑓: 0.087 (32 hom.)
• Consequence: HSPA5-DT ENST00000468244.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04

Genes affected

HSPA5-DT (HGNC:55645): (HSPA5 divergent transcript)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.184 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HSPA5-DT	ENST00000468244.2	n.46G>A		non_coding_transcript_exon_variant	1/3	4

Frequencies

GnomAD3 genomes AF: 0.109 AC: 16542 AN: 152036 Hom.: 1106 Cov.: 32

Gnomad AFR AF: 0.187

Gnomad AMI AF: 0.0725

Gnomad AMR AF: 0.0605

Gnomad ASJ AF: 0.104

Gnomad EAS AF: 0.154

Gnomad SAS AF: 0.118

Gnomad FIN AF: 0.0973

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.0707

Gnomad OTH AF: 0.0961

GnomAD4 exome AF: 0.0872 AC: 557 AN: 6384 Hom.: 32 Cov.: 0 AF XY: 0.0871 AC XY: 297 AN XY: 3410

Gnomad4 AFR exome AF: 0.235

Gnomad4 AMR exome AF: 0.0313

Gnomad4 ASJ exome AF: 0.121

Gnomad4 EAS exome AF: 0.148

Gnomad4 SAS exome AF: 0.0899

Gnomad4 FIN exome AF: 0.103

Gnomad4 NFE exome AF: 0.0706

Gnomad4 OTH exome AF: 0.0693

GnomAD4 genome AF: 0.109 AC: 16569 AN: 152148 Hom.: 1106 Cov.: 32 AF XY: 0.111 AC XY: 8226 AN XY: 74374

Gnomad4 AFR AF: 0.188

Gnomad4 AMR AF: 0.0603

Gnomad4 ASJ AF: 0.104

Gnomad4 EAS AF: 0.154

Gnomad4 SAS AF: 0.119

Gnomad4 FIN AF: 0.0973

Gnomad4 NFE AF: 0.0707

Gnomad4 OTH AF: 0.0941

Alfa AF: 0.0967 Hom.: 111

Bravo AF: 0.110

Asia WGS AF: 0.133 AC: 461 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
Cadd	Benign	0.23
Dann	Benign	0.92
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17840762; hg19: chr9-128003987;