rs3936759

chr18-54436061-T-C

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 0.906 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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.895

Gnomad4 AMR AF: 0.921

Gnomad4 ASJ AF: 0.908

Gnomad4 EAS AF: 0.996

Gnomad4 SAS AF: 0.891

Gnomad4 FIN AF: 0.931

Gnomad4 NFE AF: 0.903

Gnomad4 OTH AF: 0.891

Alfa AF: 0.905 Hom.: 32965

Bravo AF: 0.905

Asia WGS AF: 0.904 AC: 3140 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	1.1
Dann	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3936759; hg19: chr18-51962431;