chr16-56359279-T-C

Variant names:

• chr16-56359279-T-C
• rs922446

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 0.649 in 150,918 control chromosomes in the GnomAD database, including 33,575 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 0.65 (33575 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.73
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.07).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.87 is higher than 0.05.

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: 0.649 AC: 97885 AN: 150820 Hom.: 33534 Cov.: 28

Gnomad AFR AF: 0.878

Gnomad AMI AF: 0.586

Gnomad AMR AF: 0.593

Gnomad ASJ AF: 0.509

Gnomad EAS AF: 0.594

Gnomad SAS AF: 0.721

Gnomad FIN AF: 0.436

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.564

Gnomad OTH AF: 0.620

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

GnomAD4 genome AF: 0.649 AC: 97968 AN: 150918 Hom.: 33575 Cov.: 28 AF XY: 0.644 AC XY: 47417 AN XY: 73604

African (AFR) AF: 0.878 AC: 36064 AN: 41086

American (AMR) AF: 0.593 AC: 9013 AN: 15200

Ashkenazi Jewish (ASJ) AF: 0.509 AC: 1760 AN: 3460

East Asian (EAS) AF: 0.594 AC: 3053 AN: 5144

South Asian (SAS) AF: 0.720 AC: 3442 AN: 4778

European-Finnish (FIN) AF: 0.436 AC: 4428 AN: 10166

Middle Eastern (MID) AF: 0.503 AC: 147 AN: 292

European-Non Finnish (NFE) AF: 0.564 AC: 38233 AN: 67792

Other (OTH) AF: 0.620 AC: 1294 AN: 2088

Alfa AF: 0.448 Hom.: 1111

Bravo AF: 0.669

Asia WGS AF: 0.707 AC: 2458 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.20
DANN	Benign	0.32
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs922446; hg19: chr16-56393191;