5-56699208-T-G

Variant names:

• chr5-56699208-T-G
• rs16886113
• ENST00000821819.1:n.62-22680A>C

Variant summary

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

The ENST00000821819.1(ENSG00000306891):​n.62-22680A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0832 in 152,252 control chromosomes in the GnomAD database, including 582 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 0.083 (582 hom., cov: 32)
• Consequence: ENSG00000306891 ENST00000821819.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.502
• Publications: 18 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=-0.68).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.124 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.62-22680A>C		intron	N/A
	ENSG00000306891	ENST00000821820.1		n.94-16554A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0829 AC: 12619 AN: 152134 Hom.: 575 Cov.: 32

Gnomad AFR AF: 0.114

Gnomad AMI AF: 0.0340

Gnomad AMR AF: 0.0679

Gnomad ASJ AF: 0.0769

Gnomad EAS AF: 0.133

Gnomad SAS AF: 0.0707

Gnomad FIN AF: 0.0496

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0710

Gnomad OTH AF: 0.0785

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

GnomAD4 genome AF: 0.0832 AC: 12664 AN: 152252 Hom.: 582 Cov.: 32 AF XY: 0.0825 AC XY: 6140 AN XY: 74442

African (AFR) AF: 0.115 AC: 4763 AN: 41530

American (AMR) AF: 0.0678 AC: 1038 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0769 AC: 267 AN: 3470

East Asian (EAS) AF: 0.133 AC: 686 AN: 5176

South Asian (SAS) AF: 0.0708 AC: 342 AN: 4832

European-Finnish (FIN) AF: 0.0496 AC: 526 AN: 10602

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.0710 AC: 4828 AN: 68024

Other (OTH) AF: 0.0806 AC: 170 AN: 2110

Alfa AF: 0.0741 Hom.: 1510

Bravo AF: 0.0871

Asia WGS AF: 0.115 AC: 399 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	6.8
DANN	Benign	0.69
PhyloP100		-0.50

Splicing

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

Other links and lift over

dbSNP: rs16886113; hg19: chr5-55995035;