ENST00000821819.1:n.62-11501A>G

Variant names:

• chr5-56688029-T-C
• rs16886034
• ENST00000821819.1:n.62-11501A>G

Variant summary

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

The ENST00000821819.1(ENSG00000306891):​n.62-11501A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0557 in 152,234 control chromosomes in the GnomAD database, including 280 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 0.056 (280 hom., cov: 32)
• Consequence: ENSG00000306891 ENST00000821819.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.308
• Publications: 16 publications found

Genes affected

ENSG00000306891 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0969 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000821819.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000306891	ENST00000821819.1		n.62-11501A>G		intron	N/A
	ENSG00000306891	ENST00000821820.1		n.94-5375A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0557 AC: 8476 AN: 152116 Hom.: 280 Cov.: 32

Gnomad AFR AF: 0.0244

Gnomad AMI AF: 0.0330

Gnomad AMR AF: 0.0612

Gnomad ASJ AF: 0.0496

Gnomad EAS AF: 0.105

Gnomad SAS AF: 0.0894

Gnomad FIN AF: 0.0592

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0676

Gnomad OTH AF: 0.0572

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

GnomAD4 genome AF: 0.0557 AC: 8476 AN: 152234 Hom.: 280 Cov.: 32 AF XY: 0.0560 AC XY: 4167 AN XY: 74414

African (AFR) AF: 0.0244 AC: 1012 AN: 41546

American (AMR) AF: 0.0611 AC: 934 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0496 AC: 172 AN: 3468

East Asian (EAS) AF: 0.104 AC: 540 AN: 5184

South Asian (SAS) AF: 0.0893 AC: 430 AN: 4816

European-Finnish (FIN) AF: 0.0592 AC: 628 AN: 10610

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.0676 AC: 4595 AN: 68012

Other (OTH) AF: 0.0594 AC: 125 AN: 2104

Alfa AF: 0.0643 Hom.: 440

Bravo AF: 0.0547

Asia WGS AF: 0.105 AC: 365 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.5
DANN	Benign	0.73
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs16886034; hg19: chr5-55983856;