rs16947096

Variant names:

• chr16-78081777-C-T
• rs16947096

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 0.368 in 151,934 control chromosomes in the GnomAD database, including 11,120 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 (11120 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.136
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.473 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: 0.368 AC: 55909 AN: 151816 Hom.: 11109 Cov.: 31

Gnomad AFR AF: 0.207

Gnomad AMI AF: 0.348

Gnomad AMR AF: 0.375

Gnomad ASJ AF: 0.460

Gnomad EAS AF: 0.489

Gnomad SAS AF: 0.332

Gnomad FIN AF: 0.455

Gnomad MID AF: 0.334

Gnomad NFE AF: 0.441

Gnomad OTH AF: 0.352

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

GnomAD4 genome AF: 0.368 AC: 55953 AN: 151934 Hom.: 11120 Cov.: 31 AF XY: 0.369 AC XY: 27410 AN XY: 74218

African (AFR) AF: 0.207 AC: 8588 AN: 41430

American (AMR) AF: 0.375 AC: 5729 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.460 AC: 1595 AN: 3470

East Asian (EAS) AF: 0.489 AC: 2514 AN: 5140

South Asian (SAS) AF: 0.332 AC: 1596 AN: 4810

European-Finnish (FIN) AF: 0.455 AC: 4794 AN: 10538

Middle Eastern (MID) AF: 0.336 AC: 98 AN: 292

European-Non Finnish (NFE) AF: 0.441 AC: 29977 AN: 67960

Other (OTH) AF: 0.353 AC: 745 AN: 2110

Alfa AF: 0.409 Hom.: 22488

Bravo AF: 0.357

Asia WGS AF: 0.360 AC: 1252 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.51
DANN	Benign	0.49
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs16947096; hg19: chr16-78115674;