chr16-69508473-A-C

Variant names:

• chr16-69508473-A-C
• rs744972

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 151,986 control chromosomes in the GnomAD database, including 7,054 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 (7054 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.07
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.419 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.290 AC: 44103 AN: 151868 Hom.: 7056 Cov.: 31

Gnomad AFR AF: 0.425

Gnomad AMI AF: 0.272

Gnomad AMR AF: 0.188

Gnomad ASJ AF: 0.274

Gnomad EAS AF: 0.0632

Gnomad SAS AF: 0.294

Gnomad FIN AF: 0.222

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.261

Gnomad OTH AF: 0.271

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

GnomAD4 genome AF: 0.290 AC: 44112 AN: 151986 Hom.: 7054 Cov.: 31 AF XY: 0.283 AC XY: 21041 AN XY: 74276

African (AFR) AF: 0.424 AC: 17565 AN: 41414

American (AMR) AF: 0.188 AC: 2876 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.274 AC: 949 AN: 3468

East Asian (EAS) AF: 0.0628 AC: 325 AN: 5174

South Asian (SAS) AF: 0.295 AC: 1421 AN: 4822

European-Finnish (FIN) AF: 0.222 AC: 2349 AN: 10560

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.261 AC: 17742 AN: 67956

Other (OTH) AF: 0.270 AC: 569 AN: 2110

Alfa AF: 0.265 Hom.: 12072

Bravo AF: 0.290

Asia WGS AF: 0.222 AC: 771 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.56
DANN	Benign	0.77
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs744972; hg19: chr16-69542376;