16-3930444-T-C

Variant names:

• chr16-3930444-T-C
• rs8049367

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 0.375 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
• Publications: 25 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.322 AC: 13370 AN: 41464

American (AMR) AF: 0.308 AC: 4703 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.467 AC: 1618 AN: 3466

East Asian (EAS) AF: 0.666 AC: 3445 AN: 5172

South Asian (SAS) AF: 0.527 AC: 2542 AN: 4820

European-Finnish (FIN) AF: 0.352 AC: 3713 AN: 10536

Middle Eastern (MID) AF: 0.480 AC: 141 AN: 294

European-Non Finnish (NFE) AF: 0.389 AC: 26425 AN: 67960

Other (OTH) AF: 0.394 AC: 832 AN: 2110

Alfa AF: 0.398 Hom.: 23724

Bravo AF: 0.365

Asia WGS AF: 0.569 AC: 1973 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.7
DANN	Benign	0.25
PhyloP100		-0.38

Splicing

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

Other links and lift over

dbSNP: rs8049367; hg19: chr16-3980445;