rs1942919

Variant names:

• chr18-59905567-G-T
• rs1942919

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 0.327 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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.163 AC: 6763 AN: 41502

American (AMR) AF: 0.367 AC: 5603 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.503 AC: 1744 AN: 3470

East Asian (EAS) AF: 0.246 AC: 1277 AN: 5186

South Asian (SAS) AF: 0.374 AC: 1804 AN: 4826

European-Finnish (FIN) AF: 0.324 AC: 3415 AN: 10556

Middle Eastern (MID) AF: 0.541 AC: 159 AN: 294

European-Non Finnish (NFE) AF: 0.410 AC: 27901 AN: 67974

Other (OTH) AF: 0.387 AC: 818 AN: 2114

Alfa AF: 0.389 Hom.: 9582

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
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs1942919; hg19: chr18-57572799;