9-125241745-T-C

Position:

• chr9-125241745-T-C

Variant summary

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

The ENST00000468244.2(HSPA5-DT):​n.83T>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 0.71 in 156,046 control chromosomes in the GnomAD database, including 40,474 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 0.71 (39684 hom., cov: 31)
  • Exomes 𝑓: 0.62 (790 hom.)
• Consequence: HSPA5-DT ENST00000468244.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.71

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=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.879 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.83T>C		non_coding_transcript_exon_variant	1/3	4

Frequencies

GnomAD3 genomes AF: 0.712 AC: 108236 AN: 151930 Hom.: 39629 Cov.: 31

Gnomad AFR AF: 0.886

Gnomad AMI AF: 0.605

Gnomad AMR AF: 0.723

Gnomad ASJ AF: 0.576

Gnomad EAS AF: 0.703

Gnomad SAS AF: 0.664

Gnomad FIN AF: 0.756

Gnomad MID AF: 0.699

Gnomad NFE AF: 0.611

Gnomad OTH AF: 0.692

GnomAD4 exome AF: 0.621 AC: 2484 AN: 3998 Hom.: 790 Cov.: 0 AF XY: 0.622 AC XY: 1319 AN XY: 2120

Gnomad4 AFR exome AF: 0.888

Gnomad4 AMR exome AF: 0.707

Gnomad4 ASJ exome AF: 0.603

Gnomad4 EAS exome AF: 0.659

Gnomad4 SAS exome AF: 0.673

Gnomad4 FIN exome AF: 0.745

Gnomad4 NFE exome AF: 0.579

Gnomad4 OTH exome AF: 0.645

GnomAD4 genome AF: 0.713 AC: 108354 AN: 152048 Hom.: 39684 Cov.: 31 AF XY: 0.718 AC XY: 53372 AN XY: 74316

Gnomad4 AFR AF: 0.887

Gnomad4 AMR AF: 0.723

Gnomad4 ASJ AF: 0.576

Gnomad4 EAS AF: 0.704

Gnomad4 SAS AF: 0.665

Gnomad4 FIN AF: 0.756

Gnomad4 NFE AF: 0.611

Gnomad4 OTH AF: 0.689

Alfa AF: 0.625 Hom.: 50104

Bravo AF: 0.719

Asia WGS AF: 0.686 AC: 2386 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	0.23
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs391957; hg19: chr9-128004024;