rs1942569

Variant names:

• chr18-55179494-T-G
• rs1942569

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 0.447 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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.324 AC: 13448 AN: 41450

American (AMR) AF: 0.439 AC: 6705 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.566 AC: 1964 AN: 3468

East Asian (EAS) AF: 0.551 AC: 2846 AN: 5164

South Asian (SAS) AF: 0.503 AC: 2425 AN: 4822

European-Finnish (FIN) AF: 0.472 AC: 4987 AN: 10562

Middle Eastern (MID) AF: 0.565 AC: 166 AN: 294

European-Non Finnish (NFE) AF: 0.497 AC: 33761 AN: 67958

Other (OTH) AF: 0.477 AC: 1005 AN: 2108

Alfa AF: 0.486 Hom.: 46803

Bravo AF: 0.441

Asia WGS AF: 0.486 AC: 1691 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.51
CADD	Benign	13
DANN	Benign	0.91
PhyloP100		-0.51

Splicing

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

Other links and lift over

dbSNP: rs1942569; hg19: chr18-52846725;