16-50684492-C-G

Position:

• chr16-50684492-C-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 0.619 in 152,174 control chromosomes in the GnomAD database, including 30,946 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 0.62 (30946 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.533

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 = 0.728 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: 0.619 AC: 94161 AN: 152056 Hom.: 30955 Cov.: 34

Gnomad AFR AF: 0.504

Gnomad AMI AF: 0.749

Gnomad AMR AF: 0.553

Gnomad ASJ AF: 0.813

Gnomad EAS AF: 0.127

Gnomad SAS AF: 0.356

Gnomad FIN AF: 0.713

Gnomad MID AF: 0.668

Gnomad NFE AF: 0.733

Gnomad OTH AF: 0.636

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

GnomAD4 genome AF: 0.619 AC: 94173 AN: 152174 Hom.: 30946 Cov.: 34 AF XY: 0.611 AC XY: 45471 AN XY: 74410

Gnomad4 AFR AF: 0.503

Gnomad4 AMR AF: 0.553

Gnomad4 ASJ AF: 0.813

Gnomad4 EAS AF: 0.127

Gnomad4 SAS AF: 0.356

Gnomad4 FIN AF: 0.713

Gnomad4 NFE AF: 0.733

Gnomad4 OTH AF: 0.632

Alfa AF: 0.597 Hom.: 1948

Bravo AF: 0.603

Asia WGS AF: 0.248 AC: 866 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	0.28
DANN	Benign	0.23

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8043770; hg19: chr16-50718403;