chr16-82031233-G-T

Variant names:

• chr16-82031233-G-T
• rs4291899

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 0.0569 in 152,230 control chromosomes in the GnomAD database, including 351 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 0.057 (351 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0360

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0822 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: 0.0570 AC: 8672 AN: 152112 Hom.: 352 Cov.: 32

Gnomad AFR AF: 0.0157

Gnomad AMI AF: 0.0252

Gnomad AMR AF: 0.0408

Gnomad ASJ AF: 0.0274

Gnomad EAS AF: 0.000578

Gnomad SAS AF: 0.0305

Gnomad FIN AF: 0.125

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.0841

Gnomad OTH AF: 0.0420

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

GnomAD4 genome AF: 0.0569 AC: 8669 AN: 152230 Hom.: 351 Cov.: 32 AF XY: 0.0582 AC XY: 4332 AN XY: 74422

Gnomad4 AFR AF: 0.0156

Gnomad4 AMR AF: 0.0407

Gnomad4 ASJ AF: 0.0274

Gnomad4 EAS AF: 0.000580

Gnomad4 SAS AF: 0.0303

Gnomad4 FIN AF: 0.125

Gnomad4 NFE AF: 0.0841

Gnomad4 OTH AF: 0.0416

Alfa AF: 0.0690 Hom.: 551

Bravo AF: 0.0486

Asia WGS AF: 0.0150 AC: 53 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.0
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4291899; hg19: chr16-82064838;