16-24495818-A-G

Variant names:

• chr16-24495818-A-G
• rs890845

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 0.689 in 152,100 control chromosomes in the GnomAD database, including 36,513 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 (36513 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.993
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.765 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: 0.689 AC: 104678 AN: 151982 Hom.: 36468 Cov.: 32

Gnomad AFR AF: 0.772

Gnomad AMI AF: 0.829

Gnomad AMR AF: 0.681

Gnomad ASJ AF: 0.702

Gnomad EAS AF: 0.503

Gnomad SAS AF: 0.747

Gnomad FIN AF: 0.662

Gnomad MID AF: 0.807

Gnomad NFE AF: 0.651

Gnomad OTH AF: 0.705

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

GnomAD4 genome AF: 0.689 AC: 104762 AN: 152100 Hom.: 36513 Cov.: 32 AF XY: 0.691 AC XY: 51369 AN XY: 74360

African (AFR) AF: 0.772 AC: 32028 AN: 41488

American (AMR) AF: 0.680 AC: 10388 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.702 AC: 2433 AN: 3468

East Asian (EAS) AF: 0.502 AC: 2592 AN: 5160

South Asian (SAS) AF: 0.747 AC: 3606 AN: 4826

European-Finnish (FIN) AF: 0.662 AC: 6995 AN: 10574

Middle Eastern (MID) AF: 0.816 AC: 240 AN: 294

European-Non Finnish (NFE) AF: 0.651 AC: 44242 AN: 67994

Other (OTH) AF: 0.701 AC: 1482 AN: 2114

Alfa AF: 0.661 Hom.: 130072

Bravo AF: 0.688

Asia WGS AF: 0.695 AC: 2416 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	4.3
DANN	Benign	0.60
PhyloP100		-0.99

Splicing

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

Other links and lift over

dbSNP: rs890845; hg19: chr16-24507139;