rs4823568

Variant names:

• chr22-46142032-A-T
• rs4823568
• ENST00000846710.1:n.329-887T>A

Variant summary

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

The ENST00000846710.1(ENSG00000310037):​n.329-887T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.24 (3430 hom., cov: 18)
• Consequence: ENSG00000310037 ENST00000846710.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.40
• Publications: 1 publications found

Genes affected

ENSG00000310037 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.11).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.337 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000846710.1. 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
	ENSG00000310037	ENST00000846710.1		n.329-887T>A		intron	N/A
	ENSG00000310037	ENST00000846711.1		n.312-887T>A		intron	N/A
	ENSG00000310052	ENST00000846781.1		n.608-1432A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.235 AC: 28119 AN: 119620 Hom.: 3430 Cov.: 18

Gnomad AFR AF: 0.343

Gnomad AMI AF: 0.182

Gnomad AMR AF: 0.179

Gnomad ASJ AF: 0.125

Gnomad EAS AF: 0.101

Gnomad SAS AF: 0.236

Gnomad FIN AF: 0.201

Gnomad MID AF: 0.140

Gnomad NFE AF: 0.213

Gnomad OTH AF: 0.206

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

GnomAD4 genome AF: 0.235 AC: 28112 AN: 119590 Hom.: 3430 Cov.: 18 AF XY: 0.230 AC XY: 13008 AN XY: 56610

African (AFR) AF: 0.343 AC: 10055 AN: 29310

American (AMR) AF: 0.180 AC: 2137 AN: 11900

Ashkenazi Jewish (ASJ) AF: 0.125 AC: 408 AN: 3260

East Asian (EAS) AF: 0.101 AC: 426 AN: 4226

South Asian (SAS) AF: 0.235 AC: 859 AN: 3662

European-Finnish (FIN) AF: 0.201 AC: 1074 AN: 5334

Middle Eastern (MID) AF: 0.150 AC: 36 AN: 240

European-Non Finnish (NFE) AF: 0.213 AC: 12638 AN: 59234

Other (OTH) AF: 0.205 AC: 332 AN: 1618

Alfa AF: 0.0707 Hom.: 92

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	1.3
DANN	Benign	0.054
PhyloP100		-3.4

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs4823568;

hg19: chr22-46537906;