chr9-125241745-T-C

Variant names:

• chr9-125241745-T-C
• rs391957
• ENST00000468244.3:n.83T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000468244.3(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 ENST00000468244.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.71
• Publications: 46 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000468244.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HSPA5-DT	NR_186826.1		n.90T>C		non_coding_transcript_exon	Exon 1 of 3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HSPA5-DT	ENST00000468244.3	TSL:4	n.83T>C		non_coding_transcript_exon	Exon 1 of 4
	HSPA5-DT	ENST00000761981.1		n.109T>C		non_coding_transcript_exon	Exon 1 of 3
	HSPA5-DT	ENST00000761982.1		n.77T>C		non_coding_transcript_exon	Exon 1 of 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

African (AFR) AF: 0.888 AC: 87 AN: 98

American (AMR) AF: 0.707 AC: 41 AN: 58

Ashkenazi Jewish (ASJ) AF: 0.603 AC: 82 AN: 136

East Asian (EAS) AF: 0.659 AC: 207 AN: 314

South Asian (SAS) AF: 0.673 AC: 167 AN: 248

European-Finnish (FIN) AF: 0.745 AC: 298 AN: 400

Middle Eastern (MID) AF: 0.500 AC: 11 AN: 22

European-Non Finnish (NFE) AF: 0.579 AC: 1449 AN: 2502

Other (OTH) AF: 0.645 AC: 142 AN: 220

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

African (AFR) AF: 0.887 AC: 36789 AN: 41496

American (AMR) AF: 0.723 AC: 11048 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.576 AC: 1996 AN: 3466

East Asian (EAS) AF: 0.704 AC: 3622 AN: 5148

South Asian (SAS) AF: 0.665 AC: 3204 AN: 4820

European-Finnish (FIN) AF: 0.756 AC: 7984 AN: 10558

Middle Eastern (MID) AF: 0.701 AC: 206 AN: 294

European-Non Finnish (NFE) AF: 0.611 AC: 41500 AN: 67970

Other (OTH) AF: 0.689 AC: 1456 AN: 2114

Alfa AF: 0.643 Hom.: 119715

Bravo AF: 0.719

Asia WGS AF: 0.686 AC: 2386 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	0.23
DANN	Benign	0.54
PhyloP100		-3.7
PromoterAI		0.025	Neutral

Splicing

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

Other links and lift over

dbSNP: rs391957; hg19: chr9-128004024;