rs1942919

Variant names:

• chr18-59905567-G-T
• rs1942919

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;