16-22677748-G-C

Variant names:

• chr16-22677748-G-C
• rs154554

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 0.958 in 152,390 control chromosomes in the GnomAD database, including 69,828 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 0.96 (69828 hom., cov: 60)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.724

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.959 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: 0.958 AC: 145899 AN: 152272 Hom.: 69769 Cov.: 60

Gnomad AFR AF: 0.954

Gnomad AMI AF: 0.970

Gnomad AMR AF: 0.972

Gnomad ASJ AF: 0.918

Gnomad EAS AF: 0.945

Gnomad SAS AF: 0.927

Gnomad FIN AF: 0.972

Gnomad MID AF: 0.940

Gnomad NFE AF: 0.960

Gnomad OTH AF: 0.959

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

GnomAD4 genome AF: 0.958 AC: 146017 AN: 152390 Hom.: 69828 Cov.: 60 AF XY: 0.958 AC XY: 71410 AN XY: 74520

Gnomad4 AFR AF: 0.954

Gnomad4 AMR AF: 0.972

Gnomad4 ASJ AF: 0.918

Gnomad4 EAS AF: 0.946

Gnomad4 SAS AF: 0.927

Gnomad4 FIN AF: 0.972

Gnomad4 NFE AF: 0.960

Gnomad4 OTH AF: 0.959

Alfa AF: 0.969 Hom.: 2271

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.8
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs154554; hg19: chr16-22689069;