16-24496796-A-G

Variant names:

• chr16-24496796-A-G
• rs11649538

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 0.694 in 151,826 control chromosomes in the GnomAD database, including 37,067 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 0.69 (37067 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.876
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.785 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.694 AC: 105313 AN: 151706 Hom.: 37022 Cov.: 30

Gnomad AFR AF: 0.792

Gnomad AMI AF: 0.830

Gnomad AMR AF: 0.684

Gnomad ASJ AF: 0.702

Gnomad EAS AF: 0.490

Gnomad SAS AF: 0.748

Gnomad FIN AF: 0.661

Gnomad MID AF: 0.812

Gnomad NFE AF: 0.651

Gnomad OTH AF: 0.707

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

GnomAD4 genome AF: 0.694 AC: 105397 AN: 151826 Hom.: 37067 Cov.: 30 AF XY: 0.696 AC XY: 51620 AN XY: 74178

African (AFR) AF: 0.792 AC: 32819 AN: 41440

American (AMR) AF: 0.684 AC: 10420 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.702 AC: 2432 AN: 3464

East Asian (EAS) AF: 0.490 AC: 2517 AN: 5138

South Asian (SAS) AF: 0.748 AC: 3603 AN: 4816

European-Finnish (FIN) AF: 0.661 AC: 6954 AN: 10528

Middle Eastern (MID) AF: 0.822 AC: 240 AN: 292

European-Non Finnish (NFE) AF: 0.651 AC: 44170 AN: 67880

Other (OTH) AF: 0.703 AC: 1487 AN: 2114

Alfa AF: 0.664 Hom.: 56300

Bravo AF: 0.694

Asia WGS AF: 0.693 AC: 2409 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.76
DANN	Benign	0.79
PhyloP100		-0.88

Splicing

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

Other links and lift over

dbSNP: rs11649538; hg19: chr16-24508117;