rs56240109

Positions:

• chr16-3719580-A-G

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;