rs1944566

Variant names:

• chr18-77365362-C-T
• rs1944566

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 0.821 in 152,250 control chromosomes in the GnomAD database, including 51,454 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 0.82 (51454 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.670
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.835 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: 0.821 AC: 124837 AN: 152132 Hom.: 51415 Cov.: 33

Gnomad AFR AF: 0.843

Gnomad AMI AF: 0.982

Gnomad AMR AF: 0.778

Gnomad ASJ AF: 0.878

Gnomad EAS AF: 0.695

Gnomad SAS AF: 0.591

Gnomad FIN AF: 0.817

Gnomad MID AF: 0.820

Gnomad NFE AF: 0.839

Gnomad OTH AF: 0.810

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

GnomAD4 genome AF: 0.821 AC: 124927 AN: 152250 Hom.: 51454 Cov.: 33 AF XY: 0.814 AC XY: 60586 AN XY: 74458

African (AFR) AF: 0.842 AC: 35004 AN: 41554

American (AMR) AF: 0.778 AC: 11896 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.878 AC: 3046 AN: 3470

East Asian (EAS) AF: 0.694 AC: 3589 AN: 5174

South Asian (SAS) AF: 0.591 AC: 2852 AN: 4822

European-Finnish (FIN) AF: 0.817 AC: 8658 AN: 10602

Middle Eastern (MID) AF: 0.810 AC: 238 AN: 294

European-Non Finnish (NFE) AF: 0.839 AC: 57030 AN: 68012

Other (OTH) AF: 0.813 AC: 1718 AN: 2114

Alfa AF: 0.822 Hom.: 19349

Bravo AF: 0.821

Asia WGS AF: 0.665 AC: 2312 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.36
DANN	Benign	0.79
PhyloP100		-0.67

Splicing

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

Other links and lift over

dbSNP: rs1944566; hg19: chr18-75077318;