rs1942919

chr18-59905567-G-T

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 0.327 in 152,110 control chromosomes in the GnomAD database, including 9,072 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 0.33 (9072 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.215

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.406 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: 0.327 AC: 49769 AN: 151992 Hom.: 9063 Cov.: 33

Gnomad AFR AF: 0.163

Gnomad AMI AF: 0.341

Gnomad AMR AF: 0.367

Gnomad ASJ AF: 0.503

Gnomad EAS AF: 0.245

Gnomad SAS AF: 0.372

Gnomad FIN AF: 0.324

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.410

Gnomad OTH AF: 0.388

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

GnomAD4 genome AF: 0.327 AC: 49794 AN: 152110 Hom.: 9072 Cov.: 33 AF XY: 0.325 AC XY: 24190 AN XY: 74332

Gnomad4 AFR AF: 0.163

Gnomad4 AMR AF: 0.367

Gnomad4 ASJ AF: 0.503

Gnomad4 EAS AF: 0.246

Gnomad4 SAS AF: 0.374

Gnomad4 FIN AF: 0.324

Gnomad4 NFE AF: 0.410

Gnomad4 OTH AF: 0.387

Alfa AF: 0.387 Hom.: 7232

Bravo AF: 0.322

Asia WGS AF: 0.327 AC: 1140 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	2.8
Dann	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1942919; hg19: chr18-57572799;