rs1119132

Variant names:

• chr16-27392148-A-G
• rs1119132

Your query was ambiguous. Multiple possible variants found:

• chr16-27392148-A-G
• chr16-27392148-A-T

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	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

Gnomad4 AFR AF: 0.945

Gnomad4 AMR AF: 0.865

Gnomad4 ASJ AF: 0.848

Gnomad4 EAS AF: 0.695

Gnomad4 SAS AF: 0.852

Gnomad4 FIN AF: 0.910

Gnomad4 NFE AF: 0.865

Gnomad4 OTH AF: 0.872

Alfa AF: 0.880 Hom.: 15522

Bravo AF: 0.879

Asia WGS AF: 0.809 AC: 2815 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1119132; hg19: chr16-27403469;