rs17840761

Positions:

• chr9-125241700-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.38G>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 0.546 in 159,462 control chromosomes in the GnomAD database, including 24,027 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 0.55 (23009 hom., cov: 32)
  • Exomes 𝑓: 0.51 (1018 hom.)
• Consequence: HSPA5-DT ENST00000468244.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0330

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=-0.7).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.549 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
HSPA5-DT	ENST00000468244.2	n.38G>A		non_coding_transcript_exon_variant	1/3	4

Frequencies

GnomAD3 genomes AF: 0.548 AC: 83237 AN: 151860 Hom.: 22995 Cov.: 32

Gnomad AFR AF: 0.553

Gnomad AMI AF: 0.530

Gnomad AMR AF: 0.558

Gnomad ASJ AF: 0.466

Gnomad EAS AF: 0.464

Gnomad SAS AF: 0.521

Gnomad FIN AF: 0.658

Gnomad MID AF: 0.579

Gnomad NFE AF: 0.538

Gnomad OTH AF: 0.553

GnomAD4 exome AF: 0.510 AC: 3820 AN: 7484 Hom.: 1018 Cov.: 0 AF XY: 0.505 AC XY: 2034 AN XY: 4028

Gnomad4 AFR exome AF: 0.529

Gnomad4 AMR exome AF: 0.636

Gnomad4 ASJ exome AF: 0.416

Gnomad4 EAS exome AF: 0.416

Gnomad4 SAS exome AF: 0.551

Gnomad4 FIN exome AF: 0.626

Gnomad4 NFE exome AF: 0.501

Gnomad4 OTH exome AF: 0.516

GnomAD4 genome AF: 0.548 AC: 83293 AN: 151978 Hom.: 23009 Cov.: 32 AF XY: 0.551 AC XY: 40945 AN XY: 74272

Gnomad4 AFR AF: 0.553

Gnomad4 AMR AF: 0.559

Gnomad4 ASJ AF: 0.466

Gnomad4 EAS AF: 0.465

Gnomad4 SAS AF: 0.521

Gnomad4 FIN AF: 0.658

Gnomad4 NFE AF: 0.538

Gnomad4 OTH AF: 0.553

Alfa AF: 0.544 Hom.: 2840

Bravo AF: 0.541

Asia WGS AF: 0.490 AC: 1707 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	3.6
DANN	Benign	0.71
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: rs17840761; hg19: chr9-128003979;