chr18-55163048-A-G

Variant names:

• chr18-55163048-A-G
• rs9965625

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 0.543 in 152,002 control chromosomes in the GnomAD database, including 22,753 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 (22753 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.53
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.568 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.543 AC: 82514 AN: 151884 Hom.: 22740 Cov.: 32

Gnomad AFR AF: 0.565

Gnomad AMI AF: 0.641

Gnomad AMR AF: 0.480

Gnomad ASJ AF: 0.552

Gnomad EAS AF: 0.375

Gnomad SAS AF: 0.349

Gnomad FIN AF: 0.512

Gnomad MID AF: 0.618

Gnomad NFE AF: 0.573

Gnomad OTH AF: 0.552

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

GnomAD4 genome AF: 0.543 AC: 82552 AN: 152002 Hom.: 22753 Cov.: 32 AF XY: 0.535 AC XY: 39728 AN XY: 74290

African (AFR) AF: 0.565 AC: 23434 AN: 41458

American (AMR) AF: 0.479 AC: 7316 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.552 AC: 1918 AN: 3472

East Asian (EAS) AF: 0.374 AC: 1931 AN: 5158

South Asian (SAS) AF: 0.350 AC: 1689 AN: 4826

European-Finnish (FIN) AF: 0.512 AC: 5406 AN: 10550

Middle Eastern (MID) AF: 0.599 AC: 175 AN: 292

European-Non Finnish (NFE) AF: 0.573 AC: 38945 AN: 67954

Other (OTH) AF: 0.546 AC: 1153 AN: 2112

Alfa AF: 0.554 Hom.: 3746

Bravo AF: 0.545

Asia WGS AF: 0.397 AC: 1379 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.0030
DANN	Benign	0.25
PhyloP100		-4.5

Splicing

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

Other links and lift over

dbSNP: rs9965625; hg19: chr18-52830279;