22-42522853-A-G

Variant names:

• chr22-42522853-A-G
• rs5751296
• ENST00000729859.1:n.51+3500A>G

Variant summary

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

The ENST00000729859.1(ENSG00000295412):​n.51+3500A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.242 in 151,716 control chromosomes in the GnomAD database, including 4,119 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 0.24 (4119 hom., cov: 34)
• Consequence: ENSG00000295412 ENST00000729859.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.164
• Publications: 3 publications found

Genes affected

ENSG00000295412 (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 (AFR) allele frequency at 95% confidence interval = 0.339 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000729859.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000295412	ENST00000729859.1		n.51+3500A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.242 AC: 36731 AN: 151598 Hom.: 4112 Cov.: 34

Gnomad AFR AF: 0.344

Gnomad AMI AF: 0.224

Gnomad AMR AF: 0.156

Gnomad ASJ AF: 0.205

Gnomad EAS AF: 0.150

Gnomad SAS AF: 0.231

Gnomad FIN AF: 0.193

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.218

Gnomad OTH AF: 0.228

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

GnomAD4 genome AF: 0.242 AC: 36770 AN: 151716 Hom.: 4119 Cov.: 34 AF XY: 0.240 AC XY: 17771 AN XY: 74152

African (AFR) AF: 0.344 AC: 14219 AN: 41336

American (AMR) AF: 0.155 AC: 2369 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.205 AC: 712 AN: 3468

East Asian (EAS) AF: 0.151 AC: 775 AN: 5146

South Asian (SAS) AF: 0.232 AC: 1113 AN: 4800

European-Finnish (FIN) AF: 0.193 AC: 2039 AN: 10552

Middle Eastern (MID) AF: 0.224 AC: 65 AN: 290

European-Non Finnish (NFE) AF: 0.218 AC: 14779 AN: 67838

Other (OTH) AF: 0.235 AC: 495 AN: 2108

Alfa AF: 0.0906 Hom.: 56

Asia WGS AF: 0.211 AC: 734 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	5.3
DANN	Benign	0.89
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs5751296; hg19: chr22-42918859; COSMIC: COSV107386993;