5-8092964-C-T

Variant names:

• chr5-8092964-C-T
• rs10475407
• ENST00000830491.1:n.213+18383C>T

Variant summary

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

The ENST00000830491.1(ENSG00000308020):​n.213+18383C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.594 in 152,030 control chromosomes in the GnomAD database, including 27,580 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 0.59 (27580 hom., cov: 33)
• Consequence: ENSG00000308020 ENST00000830491.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.25
• Publications: 2 publications found

Genes affected

ENSG00000308020 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.89 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000830491.1. 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
	ENSG00000308020	ENST00000830491.1		n.213+18383C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.594 AC: 90213 AN: 151914 Hom.: 27571 Cov.: 33

Gnomad AFR AF: 0.476

Gnomad AMI AF: 0.566

Gnomad AMR AF: 0.639

Gnomad ASJ AF: 0.634

Gnomad EAS AF: 0.912

Gnomad SAS AF: 0.669

Gnomad FIN AF: 0.665

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.613

Gnomad OTH AF: 0.610

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

GnomAD4 genome AF: 0.594 AC: 90254 AN: 152030 Hom.: 27580 Cov.: 33 AF XY: 0.602 AC XY: 44763 AN XY: 74310

African (AFR) AF: 0.475 AC: 19695 AN: 41432

American (AMR) AF: 0.640 AC: 9768 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.634 AC: 2198 AN: 3466

East Asian (EAS) AF: 0.912 AC: 4716 AN: 5170

South Asian (SAS) AF: 0.670 AC: 3225 AN: 4816

European-Finnish (FIN) AF: 0.665 AC: 7027 AN: 10570

Middle Eastern (MID) AF: 0.595 AC: 175 AN: 294

European-Non Finnish (NFE) AF: 0.613 AC: 41657 AN: 67994

Other (OTH) AF: 0.607 AC: 1279 AN: 2106

Alfa AF: 0.604 Hom.: 19688

Bravo AF: 0.588

Asia WGS AF: 0.765 AC: 2663 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.1
DANN	Benign	0.33
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs10475407; hg19: chr5-8093077;