rs9954649

Variant names:

• chr18-23033307-G-A
• rs9954649

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 0.492 in 152,056 control chromosomes in the GnomAD database, including 21,696 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 0.49 (21696 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.19
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.636 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: 0.492 AC: 74750 AN: 151938 Hom.: 21698 Cov.: 32

Gnomad AFR AF: 0.162

Gnomad AMI AF: 0.526

Gnomad AMR AF: 0.561

Gnomad ASJ AF: 0.678

Gnomad EAS AF: 0.473

Gnomad SAS AF: 0.549

Gnomad FIN AF: 0.626

Gnomad MID AF: 0.674

Gnomad NFE AF: 0.641

Gnomad OTH AF: 0.560

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

GnomAD4 genome AF: 0.492 AC: 74749 AN: 152056 Hom.: 21696 Cov.: 32 AF XY: 0.494 AC XY: 36719 AN XY: 74338

African (AFR) AF: 0.161 AC: 6699 AN: 41492

American (AMR) AF: 0.560 AC: 8539 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.678 AC: 2353 AN: 3470

East Asian (EAS) AF: 0.473 AC: 2445 AN: 5172

South Asian (SAS) AF: 0.550 AC: 2650 AN: 4820

European-Finnish (FIN) AF: 0.626 AC: 6607 AN: 10548

Middle Eastern (MID) AF: 0.667 AC: 196 AN: 294

European-Non Finnish (NFE) AF: 0.641 AC: 43604 AN: 67984

Other (OTH) AF: 0.557 AC: 1176 AN: 2112

Alfa AF: 0.598 Hom.: 14593

Bravo AF: 0.469

Asia WGS AF: 0.489 AC: 1701 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.26
DANN	Benign	0.52
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs9954649; hg19: chr18-20613270;