rs1119132

chr16-27392148-A-Gchr16-27392148-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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;