rs136457

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr22-32188672-A-G
• chr22-32188672-A-T

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000275656 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000275656	ENST00000618747.1	n.-185T>C		upstream_gene_variant		6

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

Gnomad4 AFR AF: 0.780

Gnomad4 AMR AF: 0.426

Gnomad4 ASJ AF: 0.504

Gnomad4 EAS AF: 0.141

Gnomad4 SAS AF: 0.382

Gnomad4 FIN AF: 0.384

Gnomad4 NFE AF: 0.485

Gnomad4 OTH AF: 0.506

Alfa AF: 0.401 Hom.: 1638

Bravo AF: 0.550

Asia WGS AF: 0.352 AC: 1222 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs136457; hg19: chr22-32584659;