rs1942239

chr18-35803827-G-Achr18-35803827-G-C

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.474

Gnomad4 AMR AF: 0.301

Gnomad4 ASJ AF: 0.440

Gnomad4 EAS AF: 0.326

Gnomad4 SAS AF: 0.388

Gnomad4 FIN AF: 0.343

Gnomad4 NFE AF: 0.349

Gnomad4 OTH AF: 0.375

Alfa AF: 0.336 Hom.: 3869

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1942239; hg19: chr18-33383791;