rs1944566

Variant names:

• chr18-77365362-C-T
• rs1944566

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 0.821 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.821 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

Gnomad4 AFR AF: 0.842

Gnomad4 AMR AF: 0.778

Gnomad4 ASJ AF: 0.878

Gnomad4 EAS AF: 0.694

Gnomad4 SAS AF: 0.591

Gnomad4 FIN AF: 0.817

Gnomad4 NFE AF: 0.839

Gnomad4 OTH AF: 0.813

Alfa AF: 0.832 Hom.: 10830

Bravo AF: 0.821

Asia WGS AF: 0.665 AC: 2312 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1944566; hg19: chr18-75077318;