16-3239331-T-G

Variant names:

• chr16-3239331-T-G
• rs186493

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 0.269 in 150,084 control chromosomes in the GnomAD database, including 6,671 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 0.27 (6671 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.62
• Publications: 15 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.493 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.269 AC: 40353 AN: 149972 Hom.: 6677 Cov.: 29

Gnomad AFR AF: 0.0665

Gnomad AMI AF: 0.263

Gnomad AMR AF: 0.369

Gnomad ASJ AF: 0.265

Gnomad EAS AF: 0.510

Gnomad SAS AF: 0.292

Gnomad FIN AF: 0.398

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.329

Gnomad OTH AF: 0.283

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

GnomAD4 genome AF: 0.269 AC: 40343 AN: 150084 Hom.: 6671 Cov.: 29 AF XY: 0.275 AC XY: 20114 AN XY: 73242

African (AFR) AF: 0.0663 AC: 2686 AN: 40534

American (AMR) AF: 0.369 AC: 5550 AN: 15042

Ashkenazi Jewish (ASJ) AF: 0.265 AC: 917 AN: 3458

East Asian (EAS) AF: 0.510 AC: 2608 AN: 5116

South Asian (SAS) AF: 0.292 AC: 1395 AN: 4782

European-Finnish (FIN) AF: 0.398 AC: 4072 AN: 10220

Middle Eastern (MID) AF: 0.217 AC: 63 AN: 290

European-Non Finnish (NFE) AF: 0.329 AC: 22230 AN: 67652

Other (OTH) AF: 0.280 AC: 584 AN: 2084

Alfa AF: 0.303 Hom.: 10503

Bravo AF: 0.262

Asia WGS AF: 0.374 AC: 1298 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	5.5
DANN	Benign	0.54
PhyloP100		1.6

Splicing

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

Other links and lift over

dbSNP: rs186493; hg19: chr16-3289331;