rs56178387

Variant names:

• chr16-56638103-T-G
• rs56178387

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 0.0671 in 152,242 control chromosomes in the GnomAD database, including 492 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 0.067 (492 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.53

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.185 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: 0.0672 AC: 10216 AN: 152124 Hom.: 492 Cov.: 33

Gnomad AFR AF: 0.0172

Gnomad AMI AF: 0.0482

Gnomad AMR AF: 0.0730

Gnomad ASJ AF: 0.117

Gnomad EAS AF: 0.195

Gnomad SAS AF: 0.166

Gnomad FIN AF: 0.0225

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.0836

Gnomad OTH AF: 0.0804

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

GnomAD4 genome AF: 0.0671 AC: 10212 AN: 152242 Hom.: 492 Cov.: 33 AF XY: 0.0668 AC XY: 4968 AN XY: 74422

Gnomad4 AFR AF: 0.0172

Gnomad4 AMR AF: 0.0730

Gnomad4 ASJ AF: 0.117

Gnomad4 EAS AF: 0.195

Gnomad4 SAS AF: 0.165

Gnomad4 FIN AF: 0.0225

Gnomad4 NFE AF: 0.0836

Gnomad4 OTH AF: 0.0800

Alfa AF: 0.0682 Hom.: 58

Bravo AF: 0.0678

Asia WGS AF: 0.146 AC: 509 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.93
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs56178387; hg19: chr16-56672015;