22-32188723-G-C

Variant names:

• chr22-32188723-G-C
• rs136458
• ENST00000618747.1:n.-236C>G

Variant summary

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

The ENST00000618747.1(ENSG00000275656):​n.-236C>G variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.539 in 152,022 control chromosomes in the GnomAD database, including 24,227 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 0.54 (24227 hom., cov: 32)
• Consequence: ENSG00000275656 ENST00000618747.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.03
• Publications: 5 publications found

Genes affected

ENSG00000275656 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.773 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000618747.1. 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
	ENSG00000275656	ENST00000618747.1	TSL:6	n.-236C>G		upstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.538 AC: 81760 AN: 151906 Hom.: 24179 Cov.: 32

Gnomad AFR AF: 0.780

Gnomad AMI AF: 0.468

Gnomad AMR AF: 0.426

Gnomad ASJ AF: 0.504

Gnomad EAS AF: 0.141

Gnomad SAS AF: 0.382

Gnomad FIN AF: 0.385

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.485

Gnomad OTH AF: 0.506

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

GnomAD4 genome AF: 0.539 AC: 81865 AN: 152022 Hom.: 24227 Cov.: 32 AF XY: 0.528 AC XY: 39253 AN XY: 74300

African (AFR) AF: 0.780 AC: 32347 AN: 41476

American (AMR) AF: 0.426 AC: 6504 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.504 AC: 1746 AN: 3464

East Asian (EAS) AF: 0.141 AC: 732 AN: 5182

South Asian (SAS) AF: 0.381 AC: 1835 AN: 4810

European-Finnish (FIN) AF: 0.385 AC: 4060 AN: 10548

Middle Eastern (MID) AF: 0.541 AC: 159 AN: 294

European-Non Finnish (NFE) AF: 0.485 AC: 32988 AN: 67960

Other (OTH) AF: 0.506 AC: 1068 AN: 2112

Alfa AF: 0.343 Hom.: 806

Bravo AF: 0.550

Asia WGS AF: 0.352 AC: 1223 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.76
DANN	Benign	0.36
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs136458; hg19: chr22-32584710;