16-31336427-A-G

Position:

• chr16-31336427-A-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 0.469 in 152,120 control chromosomes in the GnomAD database, including 17,316 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 0.47 (17316 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.164

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 (EAS) allele frequency at 95% confidence interval = 0.665 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: 0.470 AC: 71413 AN: 152002 Hom.: 17321 Cov.: 33

Gnomad AFR AF: 0.393

Gnomad AMI AF: 0.431

Gnomad AMR AF: 0.422

Gnomad ASJ AF: 0.556

Gnomad EAS AF: 0.683

Gnomad SAS AF: 0.211

Gnomad FIN AF: 0.475

Gnomad MID AF: 0.598

Gnomad NFE AF: 0.524

Gnomad OTH AF: 0.492

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

GnomAD4 genome AF: 0.469 AC: 71415 AN: 152120 Hom.: 17316 Cov.: 33 AF XY: 0.464 AC XY: 34527 AN XY: 74372

Gnomad4 AFR AF: 0.392

Gnomad4 AMR AF: 0.421

Gnomad4 ASJ AF: 0.556

Gnomad4 EAS AF: 0.684

Gnomad4 SAS AF: 0.211

Gnomad4 FIN AF: 0.475

Gnomad4 NFE AF: 0.523

Gnomad4 OTH AF: 0.489

Alfa AF: 0.512 Hom.: 44536

Bravo AF: 0.470

Asia WGS AF: 0.430 AC: 1496 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.7
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3925075; hg19: chr16-31347748;