16-50684492-C-G

Variant names:

• chr16-50684492-C-G
• rs8043770

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 15 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.503 AC: 20881 AN: 41486

American (AMR) AF: 0.553 AC: 8450 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.813 AC: 2822 AN: 3470

East Asian (EAS) AF: 0.127 AC: 660 AN: 5184

South Asian (SAS) AF: 0.356 AC: 1720 AN: 4828

European-Finnish (FIN) AF: 0.713 AC: 7553 AN: 10600

Middle Eastern (MID) AF: 0.667 AC: 196 AN: 294

European-Non Finnish (NFE) AF: 0.733 AC: 49875 AN: 68010

Other (OTH) AF: 0.632 AC: 1334 AN: 2110

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
PhyloP100		0.53

Splicing

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

Other links and lift over

dbSNP: rs8043770; hg19: chr16-50718403;