16-3930444-T-C

Position:

• chr16-3930444-T-C

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 0.375 in 152,016 control chromosomes in the GnomAD database, including 11,074 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 0.38 (11074 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.383

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.648 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.375 AC: 57031 AN: 151898 Hom.: 11068 Cov.: 33

Gnomad AFR AF: 0.322

Gnomad AMI AF: 0.306

Gnomad AMR AF: 0.308

Gnomad ASJ AF: 0.467

Gnomad EAS AF: 0.666

Gnomad SAS AF: 0.528

Gnomad FIN AF: 0.352

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.389

Gnomad OTH AF: 0.388

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

GnomAD4 genome AF: 0.375 AC: 57068 AN: 152016 Hom.: 11074 Cov.: 33 AF XY: 0.375 AC XY: 27889 AN XY: 74308

Gnomad4 AFR AF: 0.322

Gnomad4 AMR AF: 0.308

Gnomad4 ASJ AF: 0.467

Gnomad4 EAS AF: 0.666

Gnomad4 SAS AF: 0.527

Gnomad4 FIN AF: 0.352

Gnomad4 NFE AF: 0.389

Gnomad4 OTH AF: 0.394

Alfa AF: 0.398 Hom.: 5900

Bravo AF: 0.365

Asia WGS AF: 0.569 AC: 1973 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.7
DANN	Benign	0.25

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8049367; hg19: chr16-3980445;