rs391957

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr9-125241745-T-A
• chr9-125241745-T-C

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000468244.3(HSPA5-DT):​n.83T>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 31)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).

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>A		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>A		non_coding_transcript_exon	Exon 1 of 4
	HSPA5-DT	ENST00000761981.1		n.109T>A		non_coding_transcript_exon	Exon 1 of 3
	HSPA5-DT	ENST00000761982.1		n.77T>A		non_coding_transcript_exon	Exon 1 of 4

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 4016 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 2134

African (AFR) AF: 0.00 AC: 0 AN: 98

American (AMR) AF: 0.00 AC: 0 AN: 60

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 138

East Asian (EAS) AF: 0.00 AC: 0 AN: 316

South Asian (SAS) AF: 0.00 AC: 0 AN: 248

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 402

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 22

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 2512

Other (OTH) AF: 0.00 AC: 0 AN: 220

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	0.21
DANN	Benign	0.58
PhyloP100		-3.7
PromoterAI		-0.023	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;