chr18-889904-A-G

Variant names:

• chr18-889904-A-G
• rs4797325

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 0.487 in 151,994 control chromosomes in the GnomAD database, including 18,742 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 (18742 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.811
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.57 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: 0.487 AC: 73936 AN: 151876 Hom.: 18749 Cov.: 32

Gnomad AFR AF: 0.354

Gnomad AMI AF: 0.551

Gnomad AMR AF: 0.449

Gnomad ASJ AF: 0.559

Gnomad EAS AF: 0.438

Gnomad SAS AF: 0.536

Gnomad FIN AF: 0.465

Gnomad MID AF: 0.585

Gnomad NFE AF: 0.574

Gnomad OTH AF: 0.498

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

GnomAD4 genome AF: 0.487 AC: 73947 AN: 151994 Hom.: 18742 Cov.: 32 AF XY: 0.479 AC XY: 35547 AN XY: 74274

African (AFR) AF: 0.353 AC: 14655 AN: 41458

American (AMR) AF: 0.448 AC: 6850 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.559 AC: 1941 AN: 3470

East Asian (EAS) AF: 0.438 AC: 2258 AN: 5150

South Asian (SAS) AF: 0.535 AC: 2574 AN: 4810

European-Finnish (FIN) AF: 0.465 AC: 4908 AN: 10548

Middle Eastern (MID) AF: 0.588 AC: 173 AN: 294

European-Non Finnish (NFE) AF: 0.574 AC: 39036 AN: 67968

Other (OTH) AF: 0.498 AC: 1051 AN: 2110

Alfa AF: 0.539 Hom.: 53360

Bravo AF: 0.479

Asia WGS AF: 0.481 AC: 1675 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.44
DANN	Benign	0.34
PhyloP100		-0.81

Splicing

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

Other links and lift over

dbSNP: rs4797325; hg19: chr18-889905;