rs9954153

Variant names:

• chr18-55871026-T-G
• rs9954153

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 0.155 in 152,126 control chromosomes in the GnomAD database, including 2,006 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 0.16 (2006 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.48
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.181 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: 0.155 AC: 23570 AN: 152008 Hom.: 2002 Cov.: 32

Gnomad AFR AF: 0.147

Gnomad AMI AF: 0.106

Gnomad AMR AF: 0.100

Gnomad ASJ AF: 0.179

Gnomad EAS AF: 0.00250

Gnomad SAS AF: 0.143

Gnomad FIN AF: 0.156

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.184

Gnomad OTH AF: 0.151

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

GnomAD4 genome AF: 0.155 AC: 23598 AN: 152126 Hom.: 2006 Cov.: 32 AF XY: 0.151 AC XY: 11222 AN XY: 74356

African (AFR) AF: 0.148 AC: 6128 AN: 41500

American (AMR) AF: 0.0998 AC: 1525 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.179 AC: 620 AN: 3468

East Asian (EAS) AF: 0.00251 AC: 13 AN: 5188

South Asian (SAS) AF: 0.144 AC: 695 AN: 4822

European-Finnish (FIN) AF: 0.156 AC: 1649 AN: 10564

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.184 AC: 12518 AN: 67986

Other (OTH) AF: 0.150 AC: 316 AN: 2110

Alfa AF: 0.175 Hom.: 1209

Bravo AF: 0.149

Asia WGS AF: 0.0830 AC: 289 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	11
DANN	Benign	0.65
PhyloP100		1.5

Splicing

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

Other links and lift over

dbSNP: rs9954153; hg19: chr18-53538257;