18-56296909-T-A

Variant names:

• chr18-56296909-T-A
• rs9959800

Variant summary

Our verdict is Benign. The variant received -9 ACMG points: 0P and 9B. BP4 BA1

The variant allele was found at a frequency of 0.424 in 152,118 control chromosomes in the GnomAD database, including 14,961 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 0.42 (14961 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.39
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -9 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.18).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.794 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.424 AC: 64422 AN: 152000 Hom.: 14950 Cov.: 32

Gnomad AFR AF: 0.253

Gnomad AMI AF: 0.632

Gnomad AMR AF: 0.378

Gnomad ASJ AF: 0.429

Gnomad EAS AF: 0.814

Gnomad SAS AF: 0.506

Gnomad FIN AF: 0.533

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.482

Gnomad OTH AF: 0.438

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

GnomAD4 genome AF: 0.424 AC: 64465 AN: 152118 Hom.: 14961 Cov.: 32 AF XY: 0.428 AC XY: 31866 AN XY: 74370

African (AFR) AF: 0.253 AC: 10517 AN: 41490

American (AMR) AF: 0.378 AC: 5785 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.429 AC: 1488 AN: 3472

East Asian (EAS) AF: 0.815 AC: 4212 AN: 5170

South Asian (SAS) AF: 0.505 AC: 2436 AN: 4824

European-Finnish (FIN) AF: 0.533 AC: 5637 AN: 10576

Middle Eastern (MID) AF: 0.408 AC: 120 AN: 294

European-Non Finnish (NFE) AF: 0.482 AC: 32772 AN: 67984

Other (OTH) AF: 0.437 AC: 923 AN: 2110

Alfa AF: 0.452 Hom.: 2037

Bravo AF: 0.403

Asia WGS AF: 0.603 AC: 2100 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.18
CADD	Benign	20
DANN	Benign	0.84
PhyloP100		2.4

Splicing

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

Other links and lift over

dbSNP: rs9959800; hg19: chr18-53964140;