16-24576962-A-C

Variant names:

• chr16-24576962-A-C
• rs9933544

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 0.29 in 151,934 control chromosomes in the GnomAD database, including 6,634 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 0.29 (6634 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.95
• Publications: 2 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 (SAS) allele frequency at 95% confidence interval = 0.334 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: 0.290 AC: 44049 AN: 151816 Hom.: 6626 Cov.: 32

Gnomad AFR AF: 0.330

Gnomad AMI AF: 0.274

Gnomad AMR AF: 0.278

Gnomad ASJ AF: 0.325

Gnomad EAS AF: 0.0919

Gnomad SAS AF: 0.348

Gnomad FIN AF: 0.174

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.296

Gnomad OTH AF: 0.290

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

GnomAD4 genome AF: 0.290 AC: 44082 AN: 151934 Hom.: 6634 Cov.: 32 AF XY: 0.285 AC XY: 21166 AN XY: 74258

African (AFR) AF: 0.330 AC: 13649 AN: 41400

American (AMR) AF: 0.277 AC: 4228 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.325 AC: 1127 AN: 3470

East Asian (EAS) AF: 0.0917 AC: 474 AN: 5170

South Asian (SAS) AF: 0.348 AC: 1674 AN: 4816

European-Finnish (FIN) AF: 0.174 AC: 1832 AN: 10550

Middle Eastern (MID) AF: 0.381 AC: 112 AN: 294

European-Non Finnish (NFE) AF: 0.296 AC: 20116 AN: 67946

Other (OTH) AF: 0.295 AC: 621 AN: 2108

Alfa AF: 0.291 Hom.: 10898

Bravo AF: 0.298

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.29
DANN	Benign	0.58
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs9933544; hg19: chr16-24588283;