rs1942569

Variant names:

• chr18-55179494-T-G
• rs1942569

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 0.447 in 152,000 control chromosomes in the GnomAD database, including 15,688 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 0.45 (15688 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.506

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.51).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.534 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: 0.447 AC: 67866 AN: 151882 Hom.: 15693 Cov.: 33

Gnomad AFR AF: 0.325

Gnomad AMI AF: 0.615

Gnomad AMR AF: 0.440

Gnomad ASJ AF: 0.566

Gnomad EAS AF: 0.552

Gnomad SAS AF: 0.503

Gnomad FIN AF: 0.472

Gnomad MID AF: 0.566

Gnomad NFE AF: 0.497

Gnomad OTH AF: 0.480

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

GnomAD4 genome AF: 0.447 AC: 67868 AN: 152000 Hom.: 15688 Cov.: 33 AF XY: 0.445 AC XY: 33028 AN XY: 74298

Gnomad4 AFR AF: 0.324

Gnomad4 AMR AF: 0.439

Gnomad4 ASJ AF: 0.566

Gnomad4 EAS AF: 0.551

Gnomad4 SAS AF: 0.503

Gnomad4 FIN AF: 0.472

Gnomad4 NFE AF: 0.497

Gnomad4 OTH AF: 0.477

Alfa AF: 0.501 Hom.: 31970

Bravo AF: 0.441

Asia WGS AF: 0.486 AC: 1691 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.51
CADD	Benign	13
DANN	Benign	0.91

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1942569; hg19: chr18-52846725;