18-35803827-G-A

Variant names:

• chr18-35803827-G-A
• rs1942239

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 0.381 in 152,050 control chromosomes in the GnomAD database, including 11,310 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 0.38 (11310 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.412
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.469 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: 0.380 AC: 57782 AN: 151932 Hom.: 11268 Cov.: 32

Gnomad AFR AF: 0.473

Gnomad AMI AF: 0.343

Gnomad AMR AF: 0.300

Gnomad ASJ AF: 0.440

Gnomad EAS AF: 0.326

Gnomad SAS AF: 0.387

Gnomad FIN AF: 0.343

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.349

Gnomad OTH AF: 0.376

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

GnomAD4 genome AF: 0.381 AC: 57893 AN: 152050 Hom.: 11310 Cov.: 32 AF XY: 0.379 AC XY: 28152 AN XY: 74318

African (AFR) AF: 0.474 AC: 19663 AN: 41454

American (AMR) AF: 0.301 AC: 4593 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.440 AC: 1525 AN: 3468

East Asian (EAS) AF: 0.326 AC: 1685 AN: 5162

South Asian (SAS) AF: 0.388 AC: 1870 AN: 4820

European-Finnish (FIN) AF: 0.343 AC: 3627 AN: 10578

Middle Eastern (MID) AF: 0.344 AC: 101 AN: 294

European-Non Finnish (NFE) AF: 0.349 AC: 23726 AN: 67970

Other (OTH) AF: 0.375 AC: 791 AN: 2110

Alfa AF: 0.340 Hom.: 4452

Bravo AF: 0.382

Asia WGS AF: 0.355 AC: 1232 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.22
DANN	Benign	0.47
PhyloP100		-0.41

Splicing

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

Other links and lift over

dbSNP: rs1942239; hg19: chr18-33383791;