9-125241700-G-A

Variant names:

• chr9-125241700-G-A
• rs17840761
• ENST00000468244.3:n.38G>A

Variant summary

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

The ENST00000468244.3(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 ENST00000468244.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0330
• Publications: 18 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=-0.7).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.549 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HSPA5-DT	NR_186826.1		n.45G>A		non_coding_transcript_exon	Exon 1 of 3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HSPA5-DT	ENST00000468244.3	TSL:4	n.38G>A		non_coding_transcript_exon	Exon 1 of 4
	HSPA5-DT	ENST00000761981.1		n.64G>A		non_coding_transcript_exon	Exon 1 of 3
	HSPA5-DT	ENST00000761982.1		n.32G>A		non_coding_transcript_exon	Exon 1 of 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

African (AFR) AF: 0.529 AC: 111 AN: 210

American (AMR) AF: 0.636 AC: 89 AN: 140

Ashkenazi Jewish (ASJ) AF: 0.416 AC: 114 AN: 274

East Asian (EAS) AF: 0.416 AC: 237 AN: 570

South Asian (SAS) AF: 0.551 AC: 292 AN: 530

European-Finnish (FIN) AF: 0.626 AC: 443 AN: 708

Middle Eastern (MID) AF: 0.450 AC: 18 AN: 40

European-Non Finnish (NFE) AF: 0.501 AC: 2319 AN: 4630

Other (OTH) AF: 0.516 AC: 197 AN: 382

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

African (AFR) AF: 0.553 AC: 22906 AN: 41416

American (AMR) AF: 0.559 AC: 8538 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.466 AC: 1618 AN: 3472

East Asian (EAS) AF: 0.465 AC: 2396 AN: 5158

South Asian (SAS) AF: 0.521 AC: 2508 AN: 4814

European-Finnish (FIN) AF: 0.658 AC: 6945 AN: 10562

Middle Eastern (MID) AF: 0.578 AC: 170 AN: 294

European-Non Finnish (NFE) AF: 0.538 AC: 36564 AN: 67964

Other (OTH) AF: 0.553 AC: 1167 AN: 2112

Alfa AF: 0.546 Hom.: 4870

Bravo AF: 0.541

Asia WGS AF: 0.490 AC: 1707 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	3.6
DANN	Benign	0.71
PhyloP100		-0.033
PromoterAI		-0.037	Neutral
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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs17840761;

hg19: chr9-128003979;