ENST00000810862.1:n.487-612G>A

Variant names:

• chr5-113694467-G-A
• rs4621553
• ENST00000810862.1:n.487-612G>A

Variant summary

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

The ENST00000810862.1(ENSG00000305424):​n.487-612G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.777 in 152,152 control chromosomes in the GnomAD database, including 46,265 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 0.78 (46265 hom., cov: 33)
• Consequence: ENSG00000305424 ENST00000810862.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.23
• Publications: 16 publications found

Genes affected

ENSG00000305424 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.921 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000810862.1. 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
	ENSG00000305424	ENST00000810862.1		n.487-612G>A		intron	N/A
	ENSG00000305424	ENST00000810863.1		n.535+3313G>A		intron	N/A
	ENSG00000305424	ENST00000810864.1		n.301-612G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.777 AC: 118127 AN: 152034 Hom.: 46237 Cov.: 33

Gnomad AFR AF: 0.774

Gnomad AMI AF: 0.750

Gnomad AMR AF: 0.655

Gnomad ASJ AF: 0.855

Gnomad EAS AF: 0.943

Gnomad SAS AF: 0.845

Gnomad FIN AF: 0.805

Gnomad MID AF: 0.788

Gnomad NFE AF: 0.781

Gnomad OTH AF: 0.775

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

GnomAD4 genome AF: 0.777 AC: 118211 AN: 152152 Hom.: 46265 Cov.: 33 AF XY: 0.776 AC XY: 57724 AN XY: 74390

African (AFR) AF: 0.774 AC: 32120 AN: 41502

American (AMR) AF: 0.655 AC: 10003 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.855 AC: 2967 AN: 3470

East Asian (EAS) AF: 0.943 AC: 4882 AN: 5178

South Asian (SAS) AF: 0.844 AC: 4075 AN: 4828

European-Finnish (FIN) AF: 0.805 AC: 8515 AN: 10576

Middle Eastern (MID) AF: 0.786 AC: 231 AN: 294

European-Non Finnish (NFE) AF: 0.781 AC: 53093 AN: 68012

Other (OTH) AF: 0.776 AC: 1641 AN: 2114

Alfa AF: 0.779 Hom.: 200533

Bravo AF: 0.762

Asia WGS AF: 0.889 AC: 3086 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	15
DANN	Benign	0.49
PhyloP100		3.2

Splicing

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

Other links and lift over

dbSNP: rs4621553; hg19: chr5-113030164;