16-22719662-C-T

Variant names:

• chr16-22719662-C-T
• rs12920706

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 0.526 in 152,042 control chromosomes in the GnomAD database, including 21,653 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 0.53 (21653 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.918
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.594 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: 0.526 AC: 79986 AN: 151924 Hom.: 21657 Cov.: 32

Gnomad AFR AF: 0.434

Gnomad AMI AF: 0.734

Gnomad AMR AF: 0.506

Gnomad ASJ AF: 0.669

Gnomad EAS AF: 0.343

Gnomad SAS AF: 0.480

Gnomad FIN AF: 0.488

Gnomad MID AF: 0.585

Gnomad NFE AF: 0.599

Gnomad OTH AF: 0.574

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

GnomAD4 genome AF: 0.526 AC: 80000 AN: 152042 Hom.: 21653 Cov.: 32 AF XY: 0.518 AC XY: 38503 AN XY: 74330

African (AFR) AF: 0.434 AC: 17973 AN: 41454

American (AMR) AF: 0.506 AC: 7737 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.669 AC: 2320 AN: 3468

East Asian (EAS) AF: 0.344 AC: 1778 AN: 5162

South Asian (SAS) AF: 0.481 AC: 2319 AN: 4820

European-Finnish (FIN) AF: 0.488 AC: 5158 AN: 10578

Middle Eastern (MID) AF: 0.588 AC: 173 AN: 294

European-Non Finnish (NFE) AF: 0.599 AC: 40676 AN: 67952

Other (OTH) AF: 0.566 AC: 1197 AN: 2114

Alfa AF: 0.577 Hom.: 67707

Bravo AF: 0.524

Asia WGS AF: 0.430 AC: 1496 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.064
DANN	Benign	0.56
PhyloP100		-0.92

Splicing

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

Other links and lift over

dbSNP: rs12920706; hg19: chr16-22730983;