chr18-9287342-G-T

Variant names:

• chr18-9287342-G-T
• rs2083845

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 0.426 in 151,824 control chromosomes in the GnomAD database, including 16,083 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 0.43 (16083 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.820
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.68 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: 0.426 AC: 64588 AN: 151706 Hom.: 16043 Cov.: 31

Gnomad AFR AF: 0.686

Gnomad AMI AF: 0.341

Gnomad AMR AF: 0.354

Gnomad ASJ AF: 0.393

Gnomad EAS AF: 0.486

Gnomad SAS AF: 0.566

Gnomad FIN AF: 0.194

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.308

Gnomad OTH AF: 0.419

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

GnomAD4 genome AF: 0.426 AC: 64672 AN: 151824 Hom.: 16083 Cov.: 31 AF XY: 0.424 AC XY: 31489 AN XY: 74236

African (AFR) AF: 0.687 AC: 28401 AN: 41350

American (AMR) AF: 0.353 AC: 5392 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.393 AC: 1363 AN: 3466

East Asian (EAS) AF: 0.485 AC: 2505 AN: 5160

South Asian (SAS) AF: 0.565 AC: 2722 AN: 4820

European-Finnish (FIN) AF: 0.194 AC: 2048 AN: 10548

Middle Eastern (MID) AF: 0.459 AC: 135 AN: 294

European-Non Finnish (NFE) AF: 0.308 AC: 20911 AN: 67910

Other (OTH) AF: 0.420 AC: 885 AN: 2106

Alfa AF: 0.347 Hom.: 13045

Bravo AF: 0.446

Asia WGS AF: 0.492 AC: 1710 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	0.68
DANN	Benign	0.60
PhyloP100		-0.82

Splicing

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

Other links and lift over

dbSNP: rs2083845; hg19: chr18-9287340;