22-32188672-A-G

Variant names:

• chr22-32188672-A-G
• rs136457
• ENST00000618747.1:n.-185T>C

Variant summary

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

The ENST00000618747.1(ENSG00000275656):​n.-185T>C variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.538 in 152,112 control chromosomes in the GnomAD database, including 24,228 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 (24228 hom., cov: 33)
• Consequence: ENSG00000275656 ENST00000618747.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.108
• Publications: 6 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=-0.69).
• 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000275656	ENST00000618747.1	TSL:6	n.-185T>C		upstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.538 AC: 81770 AN: 151994 Hom.: 24180 Cov.: 33

Gnomad AFR AF: 0.780

Gnomad AMI AF: 0.467

Gnomad AMR AF: 0.426

Gnomad ASJ AF: 0.504

Gnomad EAS AF: 0.140

Gnomad SAS AF: 0.383

Gnomad FIN AF: 0.384

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: 0.538 AC: 81875 AN: 152112 Hom.: 24228 Cov.: 33 AF XY: 0.528 AC XY: 39235 AN XY: 74336

African (AFR) AF: 0.780 AC: 32354 AN: 41494

American (AMR) AF: 0.426 AC: 6511 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.504 AC: 1748 AN: 3470

East Asian (EAS) AF: 0.141 AC: 729 AN: 5188

South Asian (SAS) AF: 0.382 AC: 1843 AN: 4824

European-Finnish (FIN) AF: 0.384 AC: 4056 AN: 10558

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

European-Non Finnish (NFE) AF: 0.485 AC: 32980 AN: 67974

Other (OTH) AF: 0.506 AC: 1069 AN: 2114

Alfa AF: 0.418 Hom.: 1882

Bravo AF: 0.550

Asia WGS AF: 0.352 AC: 1222 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	4.4
DANN	Benign	0.63
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs136457; hg19: chr22-32584659;