ENST00000485881.1:n.419T>C

Variant names:

• chr3-137880713-T-C
• rs6794514
• ENST00000485881.1:n.419T>C

Variant summary

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

The ENST00000485881.1(HSPA8P9):​n.419T>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 0.855 in 816,798 control chromosomes in the GnomAD database, including 300,103 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 0.85 (55566 hom., cov: 30)
  • Exomes 𝑓: 0.86 (244537 hom.)
• Consequence: HSPA8P9 ENST00000485881.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.53
• Publications: 3 publications found

Genes affected

HSPA8P9 (HGNC:44924): (heat shock protein family A (Hsp70) member 8 pseudogene 9)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.63).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.88 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000485881.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HSPA8P9	ENST00000485881.1	TSL:6	n.419T>C		non_coding_transcript_exon	Exon 1 of 1

Frequencies

GnomAD3 genomes AF: 0.854 AC: 129742 AN: 151888 Hom.: 55525 Cov.: 30

Gnomad AFR AF: 0.841

Gnomad AMI AF: 0.810

Gnomad AMR AF: 0.791

Gnomad ASJ AF: 0.925

Gnomad EAS AF: 0.730

Gnomad SAS AF: 0.803

Gnomad FIN AF: 0.853

Gnomad MID AF: 0.899

Gnomad NFE AF: 0.886

Gnomad OTH AF: 0.867

GnomAD4 exome AF: 0.855 AC: 568436 AN: 664792 Hom.: 244537 Cov.: 7 AF XY: 0.856 AC XY: 307836 AN XY: 359824

African (AFR) AF: 0.845 AC: 15590 AN: 18444

American (AMR) AF: 0.691 AC: 30173 AN: 43660

Ashkenazi Jewish (ASJ) AF: 0.925 AC: 19649 AN: 21238

East Asian (EAS) AF: 0.743 AC: 26920 AN: 36232

South Asian (SAS) AF: 0.808 AC: 57059 AN: 70578

European-Finnish (FIN) AF: 0.853 AC: 42444 AN: 49772

Middle Eastern (MID) AF: 0.854 AC: 3105 AN: 3636

European-Non Finnish (NFE) AF: 0.888 AC: 343665 AN: 386950

Other (OTH) AF: 0.870 AC: 29831 AN: 34282

GnomAD4 genome AF: 0.854 AC: 129839 AN: 152006 Hom.: 55566 Cov.: 30 AF XY: 0.851 AC XY: 63192 AN XY: 74278

African (AFR) AF: 0.841 AC: 34892 AN: 41470

American (AMR) AF: 0.791 AC: 12084 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.925 AC: 3210 AN: 3470

East Asian (EAS) AF: 0.730 AC: 3720 AN: 5098

South Asian (SAS) AF: 0.805 AC: 3872 AN: 4810

European-Finnish (FIN) AF: 0.853 AC: 9003 AN: 10560

Middle Eastern (MID) AF: 0.901 AC: 265 AN: 294

European-Non Finnish (NFE) AF: 0.886 AC: 60233 AN: 68004

Other (OTH) AF: 0.863 AC: 1823 AN: 2112

Alfa AF: 0.873 Hom.: 7215

Bravo AF: 0.848

Asia WGS AF: 0.776 AC: 2700 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.63
CADD	Benign	2.4
DANN	Benign	0.81
PhyloP100		1.5

Splicing

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

Other links and lift over

dbSNP: rs6794514; hg19: chr3-137599555;