rs56240109

Variant names:

• chr16-3719580-A-G
• rs56240109

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 0.0894 in 152,254 control chromosomes in the GnomAD database, including 867 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 0.089 (867 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.18

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.129 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: 0.0895 AC: 13621 AN: 152136 Hom.: 867 Cov.: 33

Gnomad AFR AF: 0.0248

Gnomad AMI AF: 0.102

Gnomad AMR AF: 0.0767

Gnomad ASJ AF: 0.156

Gnomad EAS AF: 0.00714

Gnomad SAS AF: 0.115

Gnomad FIN AF: 0.0933

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.132

Gnomad OTH AF: 0.0936

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

GnomAD4 genome AF: 0.0894 AC: 13613 AN: 152254 Hom.: 867 Cov.: 33 AF XY: 0.0872 AC XY: 6491 AN XY: 74460

Gnomad4 AFR AF: 0.0247

Gnomad4 AMR AF: 0.0765

Gnomad4 ASJ AF: 0.156

Gnomad4 EAS AF: 0.00696

Gnomad4 SAS AF: 0.116

Gnomad4 FIN AF: 0.0933

Gnomad4 NFE AF: 0.131

Gnomad4 OTH AF: 0.0926

Alfa AF: 0.112 Hom.: 141

Bravo AF: 0.0824

Asia WGS AF: 0.0610 AC: 215 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.30
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs56240109; hg19: chr16-3769581;