rs904015

Variant names:

• chr8-11789425-C-T
• rs904015
• ENST00000824450.1:n.76C>T

Variant summary

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

The ENST00000824450.1(ENSG00000307192):​n.76C>T 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 0.313 in 151,776 control chromosomes in the GnomAD database, including 7,497 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 0.31 (7497 hom., cov: 30)
• Consequence: ENSG00000307192 ENST00000824450.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.357
• Publications: 15 publications found

Genes affected

ENSG00000307192 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.345 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000824450.1. 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
	ENSG00000307192	ENST00000824450.1		n.76C>T		non_coding_transcript_exon	Exon 1 of 2

Frequencies

GnomAD3 genomes AF: 0.313 AC: 47432 AN: 151660 Hom.: 7496 Cov.: 30

Gnomad AFR AF: 0.287

Gnomad AMI AF: 0.337

Gnomad AMR AF: 0.261

Gnomad ASJ AF: 0.405

Gnomad EAS AF: 0.272

Gnomad SAS AF: 0.211

Gnomad FIN AF: 0.280

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.349

Gnomad OTH AF: 0.340

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.313 AC: 47445 AN: 151776 Hom.: 7497 Cov.: 30 AF XY: 0.305 AC XY: 22628 AN XY: 74156

African (AFR) AF: 0.287 AC: 11872 AN: 41398

American (AMR) AF: 0.260 AC: 3972 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.405 AC: 1404 AN: 3470

East Asian (EAS) AF: 0.271 AC: 1384 AN: 5100

South Asian (SAS) AF: 0.211 AC: 1014 AN: 4804

European-Finnish (FIN) AF: 0.280 AC: 2950 AN: 10550

Middle Eastern (MID) AF: 0.415 AC: 122 AN: 294

European-Non Finnish (NFE) AF: 0.349 AC: 23711 AN: 67898

Other (OTH) AF: 0.337 AC: 709 AN: 2104

Alfa AF: 0.339 Hom.: 35563

Bravo AF: 0.310

Asia WGS AF: 0.223 AC: 776 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.8
DANN	Benign	0.78
PhyloP100		-0.36

Splicing

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

Other links and lift over

dbSNP: rs904015; hg19: chr8-11646934;