16-46634557-G-T

Variant names:

• chr16-46634557-G-T
• rs56168099

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0217 in 151,602 control chromosomes in the GnomAD database, including 49 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 0.022 (49 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.656
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0217 (3290/151602) while in subpopulation NFE AF = 0.0348 (2366/67918). AF 95% confidence interval is 0.0337. There are 49 homozygotes in GnomAd4. There are 1528 alleles in the male GnomAd4 subpopulation. Median coverage is 31. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 49 gene

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.0218 AC: 3295 AN: 151486 Hom.: 50 Cov.: 31

Gnomad AFR AF: 0.00548

Gnomad AMI AF: 0.0374

Gnomad AMR AF: 0.0137

Gnomad ASJ AF: 0.00838

Gnomad EAS AF: 0.000194

Gnomad SAS AF: 0.00915

Gnomad FIN AF: 0.0310

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0348

Gnomad OTH AF: 0.0226

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

GnomAD4 genome AF: 0.0217 AC: 3290 AN: 151602 Hom.: 49 Cov.: 31 AF XY: 0.0206 AC XY: 1528 AN XY: 74044

African (AFR) AF: 0.00547 AC: 226 AN: 41342

American (AMR) AF: 0.0137 AC: 208 AN: 15196

Ashkenazi Jewish (ASJ) AF: 0.00838 AC: 29 AN: 3462

East Asian (EAS) AF: 0.000388 AC: 2 AN: 5152

South Asian (SAS) AF: 0.00895 AC: 43 AN: 4806

European-Finnish (FIN) AF: 0.0310 AC: 323 AN: 10420

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.0348 AC: 2366 AN: 67918

Other (OTH) AF: 0.0219 AC: 46 AN: 2104

Alfa AF: 0.0306 Hom.: 101

Bravo AF: 0.0204

Asia WGS AF: 0.00375 AC: 13 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.9
DANN	Benign	0.19
PhyloP100		-0.66

Splicing

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

Other links and lift over

dbSNP: rs56168099; hg19: chr16-46668469;