16-14294448-G-A

Variant names:

• chr16-14294448-G-A
• rs1659127

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 0.328 in 151,992 control chromosomes in the GnomAD database, including 8,441 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 0.33 (8441 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0950
• Publications: 73 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 (EAS) allele frequency at 95% confidence interval = 0.521 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: 0.329 AC: 49909 AN: 151874 Hom.: 8438 Cov.: 32

Gnomad AFR AF: 0.299

Gnomad AMI AF: 0.300

Gnomad AMR AF: 0.311

Gnomad ASJ AF: 0.262

Gnomad EAS AF: 0.539

Gnomad SAS AF: 0.307

Gnomad FIN AF: 0.335

Gnomad MID AF: 0.312

Gnomad NFE AF: 0.338

Gnomad OTH AF: 0.356

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

GnomAD4 genome AF: 0.328 AC: 49926 AN: 151992 Hom.: 8441 Cov.: 32 AF XY: 0.329 AC XY: 24462 AN XY: 74296

African (AFR) AF: 0.299 AC: 12388 AN: 41442

American (AMR) AF: 0.311 AC: 4752 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.262 AC: 910 AN: 3470

East Asian (EAS) AF: 0.538 AC: 2774 AN: 5156

South Asian (SAS) AF: 0.307 AC: 1477 AN: 4816

European-Finnish (FIN) AF: 0.335 AC: 3537 AN: 10558

Middle Eastern (MID) AF: 0.318 AC: 93 AN: 292

European-Non Finnish (NFE) AF: 0.338 AC: 22959 AN: 67960

Other (OTH) AF: 0.361 AC: 763 AN: 2112

Alfa AF: 0.331 Hom.: 26503

Bravo AF: 0.325

Asia WGS AF: 0.417 AC: 1452 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	1.0
DANN	Benign	0.71
PhyloP100		-0.095

Splicing

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

Other links and lift over

dbSNP: rs1659127; hg19: chr16-14388305;