chr16-3239331-T-G

Position:

• chr16-3239331-T-G

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 0.269 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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Gnomad4 AFR AF: 0.0663

Gnomad4 AMR AF: 0.369

Gnomad4 ASJ AF: 0.265

Gnomad4 EAS AF: 0.510

Gnomad4 SAS AF: 0.292

Gnomad4 FIN AF: 0.398

Gnomad4 NFE AF: 0.329

Gnomad4 OTH AF: 0.280

Alfa AF: 0.301 Hom.: 7650

Bravo AF: 0.262

Asia WGS AF: 0.374 AC: 1298 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs186493; hg19: chr16-3289331;