chr18-22591090-C-T

Variant names:

• chr18-22591090-C-T
• rs9954441

Variant summary

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

The variant allele was found at a frequency of 0.176 in 151,904 control chromosomes in the GnomAD database, including 2,591 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 0.18 (2591 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.104
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.297 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

Frequencies

GnomAD3 genomes AF: 0.176 AC: 26702 AN: 151786 Hom.: 2596 Cov.: 31

Gnomad AFR AF: 0.229

Gnomad AMI AF: 0.0855

Gnomad AMR AF: 0.186

Gnomad ASJ AF: 0.129

Gnomad EAS AF: 0.310

Gnomad SAS AF: 0.222

Gnomad FIN AF: 0.0988

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.144

Gnomad OTH AF: 0.164

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

GnomAD4 genome AF: 0.176 AC: 26694 AN: 151904 Hom.: 2591 Cov.: 31 AF XY: 0.176 AC XY: 13054 AN XY: 74226

African (AFR) AF: 0.229 AC: 9473 AN: 41414

American (AMR) AF: 0.186 AC: 2840 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.129 AC: 446 AN: 3468

East Asian (EAS) AF: 0.309 AC: 1592 AN: 5146

South Asian (SAS) AF: 0.221 AC: 1062 AN: 4800

European-Finnish (FIN) AF: 0.0988 AC: 1040 AN: 10530

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.144 AC: 9759 AN: 67966

Other (OTH) AF: 0.165 AC: 348 AN: 2112

Alfa AF: 0.0738 Hom.: 90

Bravo AF: 0.184

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.77
DANN	Benign	0.15
PhyloP100		-0.10

Splicing

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

Other links and lift over

dbSNP: rs9954441; hg19: chr18-20171053;