16-82031233-G-T

Variant names:

• chr16-82031233-G-T
• rs4291899

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.0156 AC: 650 AN: 41566

American (AMR) AF: 0.0407 AC: 622 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0274 AC: 95 AN: 3466

East Asian (EAS) AF: 0.000580 AC: 3 AN: 5176

South Asian (SAS) AF: 0.0303 AC: 146 AN: 4822

European-Finnish (FIN) AF: 0.125 AC: 1324 AN: 10584

Middle Eastern (MID) AF: 0.00340 AC: 1 AN: 294

European-Non Finnish (NFE) AF: 0.0841 AC: 5717 AN: 68006

Other (OTH) AF: 0.0416 AC: 88 AN: 2116

Alfa AF: 0.0689 Hom.: 841

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
PhyloP100		0.036

Splicing

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

Other links and lift over

dbSNP: rs4291899; hg19: chr16-82064838;