16-3153334-T-C

Variant names:

• chr16-3153334-T-C
• rs224188

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 0.76 in 151,024 control chromosomes in the GnomAD database, including 44,053 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 0.76 (44053 hom., cov: 27)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.13

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.842 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: 0.760 AC: 114667 AN: 150922 Hom.: 44018 Cov.: 27

Gnomad AFR AF: 0.653

Gnomad AMI AF: 0.873

Gnomad AMR AF: 0.813

Gnomad ASJ AF: 0.798

Gnomad EAS AF: 0.672

Gnomad SAS AF: 0.865

Gnomad FIN AF: 0.811

Gnomad MID AF: 0.867

Gnomad NFE AF: 0.799

Gnomad OTH AF: 0.780

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

GnomAD4 genome AF: 0.760 AC: 114746 AN: 151024 Hom.: 44053 Cov.: 27 AF XY: 0.763 AC XY: 56279 AN XY: 73734

Gnomad4 AFR AF: 0.654

Gnomad4 AMR AF: 0.813

Gnomad4 ASJ AF: 0.798

Gnomad4 EAS AF: 0.671

Gnomad4 SAS AF: 0.864

Gnomad4 FIN AF: 0.811

Gnomad4 NFE AF: 0.799

Gnomad4 OTH AF: 0.783

Alfa AF: 0.798 Hom.: 20552

Bravo AF: 0.753

Asia WGS AF: 0.788 AC: 2736 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.32
DANN	Benign	0.17

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs224188; hg19: chr16-3203335;