16-29005207-G-C

Variant names:

• chr16-29005207-G-C
• rs9924619

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 0.175 in 152,044 control chromosomes in the GnomAD database, including 2,813 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 0.18 (2813 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.249
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.323 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: 0.175 AC: 26619 AN: 151926 Hom.: 2797 Cov.: 32

Gnomad AFR AF: 0.222

Gnomad AMI AF: 0.0614

Gnomad AMR AF: 0.241

Gnomad ASJ AF: 0.129

Gnomad EAS AF: 0.337

Gnomad SAS AF: 0.336

Gnomad FIN AF: 0.187

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.111

Gnomad OTH AF: 0.159

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

GnomAD4 genome AF: 0.175 AC: 26664 AN: 152044 Hom.: 2813 Cov.: 32 AF XY: 0.183 AC XY: 13593 AN XY: 74316

African (AFR) AF: 0.222 AC: 9213 AN: 41432

American (AMR) AF: 0.242 AC: 3689 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.129 AC: 449 AN: 3472

East Asian (EAS) AF: 0.336 AC: 1737 AN: 5170

South Asian (SAS) AF: 0.336 AC: 1613 AN: 4804

European-Finnish (FIN) AF: 0.187 AC: 1984 AN: 10586

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.111 AC: 7561 AN: 68006

Other (OTH) AF: 0.158 AC: 334 AN: 2112

Alfa AF: 0.0544 Hom.: 46

Bravo AF: 0.181

Asia WGS AF: 0.322 AC: 1118 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	3.6
DANN	Benign	0.71
PhyloP100		0.25

Splicing

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

Other links and lift over

dbSNP: rs9924619; hg19: chr16-29016528;