chr22-45034396-C-G

Variant names:

• chr22-45034396-C-G
• rs10483226
• ENST00000836280.1:n.189-10024G>C

Variant summary

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

The ENST00000836280.1(ENSG00000308760):​n.189-10024G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.173 in 152,194 control chromosomes in the GnomAD database, including 2,508 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 0.17 (2508 hom., cov: 32)
• Consequence: ENSG00000308760 ENST00000836280.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.730
• Publications: 4 publications found

Genes affected

ENSG00000308760 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.323 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000836280.1. 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
	ENSG00000308760	ENST00000836280.1		n.189-10024G>C		intron	N/A
	ENSG00000308760	ENST00000836281.1		n.306-10024G>C		intron	N/A
	ENSG00000308760	ENST00000836282.1		n.474-10024G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.173 AC: 26355 AN: 152076 Hom.: 2499 Cov.: 32

Gnomad AFR AF: 0.170

Gnomad AMI AF: 0.229

Gnomad AMR AF: 0.237

Gnomad ASJ AF: 0.150

Gnomad EAS AF: 0.336

Gnomad SAS AF: 0.215

Gnomad FIN AF: 0.212

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.140

Gnomad OTH AF: 0.170

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

GnomAD4 genome AF: 0.173 AC: 26395 AN: 152194 Hom.: 2508 Cov.: 32 AF XY: 0.180 AC XY: 13421 AN XY: 74408

African (AFR) AF: 0.171 AC: 7084 AN: 41506

American (AMR) AF: 0.238 AC: 3640 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.150 AC: 521 AN: 3470

East Asian (EAS) AF: 0.336 AC: 1734 AN: 5164

South Asian (SAS) AF: 0.214 AC: 1034 AN: 4826

European-Finnish (FIN) AF: 0.212 AC: 2243 AN: 10602

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.140 AC: 9532 AN: 68020

Other (OTH) AF: 0.169 AC: 357 AN: 2110

Alfa AF: 0.152 Hom.: 235

Bravo AF: 0.176

Asia WGS AF: 0.255 AC: 886 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.30
DANN	Benign	0.57
PhyloP100		-0.73

Splicing

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

Other links and lift over

dbSNP: rs10483226; hg19: chr22-45430277;