16-74839676-G-A

Variant names:

• chr16-74839676-G-A
• rs725709

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 0.369 in 151,818 control chromosomes in the GnomAD database, including 10,514 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 0.37 (10514 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0120
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.473 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.369 AC: 55978 AN: 151700 Hom.: 10507 Cov.: 31

Gnomad AFR AF: 0.393

Gnomad AMI AF: 0.324

Gnomad AMR AF: 0.380

Gnomad ASJ AF: 0.289

Gnomad EAS AF: 0.489

Gnomad SAS AF: 0.478

Gnomad FIN AF: 0.423

Gnomad MID AF: 0.331

Gnomad NFE AF: 0.332

Gnomad OTH AF: 0.360

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

GnomAD4 genome AF: 0.369 AC: 56021 AN: 151818 Hom.: 10514 Cov.: 31 AF XY: 0.376 AC XY: 27881 AN XY: 74182

African (AFR) AF: 0.393 AC: 16242 AN: 41358

American (AMR) AF: 0.380 AC: 5795 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.289 AC: 1001 AN: 3468

East Asian (EAS) AF: 0.489 AC: 2521 AN: 5158

South Asian (SAS) AF: 0.477 AC: 2295 AN: 4810

European-Finnish (FIN) AF: 0.423 AC: 4452 AN: 10518

Middle Eastern (MID) AF: 0.332 AC: 97 AN: 292

European-Non Finnish (NFE) AF: 0.332 AC: 22566 AN: 67944

Other (OTH) AF: 0.360 AC: 757 AN: 2104

Alfa AF: 0.334 Hom.: 13272

Bravo AF: 0.366

Asia WGS AF: 0.442 AC: 1536 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.1
DANN	Benign	0.76
PhyloP100		-0.012

Splicing

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

Other links and lift over

dbSNP: rs725709; hg19: chr16-74873574;