rs3936759

Variant names:

• chr18-54436061-T-C
• rs3936759

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 0.906 in 152,278 control chromosomes in the GnomAD database, including 62,577 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 0.91 (62577 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.740
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.973 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.906 AC: 137915 AN: 152160 Hom.: 62528 Cov.: 34

Gnomad AFR AF: 0.895

Gnomad AMI AF: 0.778

Gnomad AMR AF: 0.921

Gnomad ASJ AF: 0.908

Gnomad EAS AF: 0.996

Gnomad SAS AF: 0.890

Gnomad FIN AF: 0.931

Gnomad MID AF: 0.867

Gnomad NFE AF: 0.903

Gnomad OTH AF: 0.892

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

GnomAD4 genome AF: 0.906 AC: 138023 AN: 152278 Hom.: 62577 Cov.: 34 AF XY: 0.908 AC XY: 67567 AN XY: 74448

African (AFR) AF: 0.895 AC: 37184 AN: 41554

American (AMR) AF: 0.921 AC: 14081 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.908 AC: 3154 AN: 3472

East Asian (EAS) AF: 0.996 AC: 5161 AN: 5184

South Asian (SAS) AF: 0.891 AC: 4298 AN: 4826

European-Finnish (FIN) AF: 0.931 AC: 9873 AN: 10610

Middle Eastern (MID) AF: 0.871 AC: 256 AN: 294

European-Non Finnish (NFE) AF: 0.903 AC: 61426 AN: 68024

Other (OTH) AF: 0.891 AC: 1884 AN: 2114

Alfa AF: 0.907 Hom.: 46891

Bravo AF: 0.905

Asia WGS AF: 0.904 AC: 3140 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.1
DANN	Benign	0.51
PhyloP100		-0.74

Splicing

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

Other links and lift over

dbSNP: rs3936759; hg19: chr18-51962431;