rs154659

Positions:

• chr16-89600929-T-C

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 0.335 in 152,146 control chromosomes in the GnomAD database, including 9,467 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 (9467 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.873

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 = 0.491 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.334 AC: 50828 AN: 152030 Hom.: 9433 Cov.: 33

Gnomad AFR AF: 0.496

Gnomad AMI AF: 0.126

Gnomad AMR AF: 0.359

Gnomad ASJ AF: 0.276

Gnomad EAS AF: 0.387

Gnomad SAS AF: 0.288

Gnomad FIN AF: 0.293

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.245

Gnomad OTH AF: 0.283

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

GnomAD4 genome AF: 0.335 AC: 50930 AN: 152146 Hom.: 9467 Cov.: 33 AF XY: 0.336 AC XY: 24962 AN XY: 74386

Gnomad4 AFR AF: 0.496

Gnomad4 AMR AF: 0.360

Gnomad4 ASJ AF: 0.276

Gnomad4 EAS AF: 0.386

Gnomad4 SAS AF: 0.288

Gnomad4 FIN AF: 0.293

Gnomad4 NFE AF: 0.245

Gnomad4 OTH AF: 0.289

Alfa AF: 0.260 Hom.: 10603

Bravo AF: 0.351

Asia WGS AF: 0.409 AC: 1420 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	0.58
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs154659; hg19: chr16-89667337;