16-22677748-G-C

Variant names:

• chr16-22677748-G-C
• rs154554

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 0.958 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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.954 AC: 39690 AN: 41592

American (AMR) AF: 0.972 AC: 14882 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.918 AC: 3186 AN: 3472

East Asian (EAS) AF: 0.946 AC: 4913 AN: 5194

South Asian (SAS) AF: 0.927 AC: 4475 AN: 4826

European-Finnish (FIN) AF: 0.972 AC: 10331 AN: 10630

Middle Eastern (MID) AF: 0.935 AC: 275 AN: 294

European-Non Finnish (NFE) AF: 0.960 AC: 65350 AN: 68046

Other (OTH) AF: 0.959 AC: 2030 AN: 2116

Alfa AF: 0.969 Hom.: 2271

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.8
DANN	Benign	0.67
PhyloP100		-0.72

Splicing

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

Other links and lift over

dbSNP: rs154554; hg19: chr16-22689069;