16-27392148-A-G

Variant names:

• chr16-27392148-A-G
• rs1119132

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 0.883 in 152,214 control chromosomes in the GnomAD database, including 59,562 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 0.88 (59562 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.502
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.937 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: 0.883 AC: 134295 AN: 152096 Hom.: 59511 Cov.: 32

Gnomad AFR AF: 0.945

Gnomad AMI AF: 0.809

Gnomad AMR AF: 0.865

Gnomad ASJ AF: 0.848

Gnomad EAS AF: 0.696

Gnomad SAS AF: 0.853

Gnomad FIN AF: 0.910

Gnomad MID AF: 0.905

Gnomad NFE AF: 0.865

Gnomad OTH AF: 0.873

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

GnomAD4 genome AF: 0.883 AC: 134403 AN: 152214 Hom.: 59562 Cov.: 32 AF XY: 0.884 AC XY: 65785 AN XY: 74420

African (AFR) AF: 0.945 AC: 39244 AN: 41542

American (AMR) AF: 0.865 AC: 13220 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.848 AC: 2944 AN: 3470

East Asian (EAS) AF: 0.695 AC: 3597 AN: 5172

South Asian (SAS) AF: 0.852 AC: 4108 AN: 4822

European-Finnish (FIN) AF: 0.910 AC: 9633 AN: 10588

Middle Eastern (MID) AF: 0.898 AC: 264 AN: 294

European-Non Finnish (NFE) AF: 0.865 AC: 58815 AN: 68020

Other (OTH) AF: 0.872 AC: 1840 AN: 2110

Alfa AF: 0.872 Hom.: 25155

Bravo AF: 0.879

Asia WGS AF: 0.809 AC: 2815 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.3
DANN	Benign	0.42
PhyloP100		-0.50

Splicing

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

Other links and lift over

dbSNP: rs1119132; hg19: chr16-27403469;