16-27370391-C-T

Variant names:

• chr16-27370391-C-T
• rs16976728

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 0.365 in 152,032 control chromosomes in the GnomAD database, including 10,263 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 0.36 (10263 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0880
• Publications: 20 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.52).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.499 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: 0.365 AC: 55392 AN: 151914 Hom.: 10249 Cov.: 32

Gnomad AFR AF: 0.295

Gnomad AMI AF: 0.514

Gnomad AMR AF: 0.368

Gnomad ASJ AF: 0.325

Gnomad EAS AF: 0.516

Gnomad SAS AF: 0.436

Gnomad FIN AF: 0.380

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.388

Gnomad OTH AF: 0.342

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

GnomAD4 genome AF: 0.365 AC: 55429 AN: 152032 Hom.: 10263 Cov.: 32 AF XY: 0.369 AC XY: 27437 AN XY: 74314

African (AFR) AF: 0.295 AC: 12224 AN: 41462

American (AMR) AF: 0.369 AC: 5634 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.325 AC: 1128 AN: 3472

East Asian (EAS) AF: 0.516 AC: 2660 AN: 5160

South Asian (SAS) AF: 0.437 AC: 2102 AN: 4814

European-Finnish (FIN) AF: 0.380 AC: 4015 AN: 10562

Middle Eastern (MID) AF: 0.432 AC: 127 AN: 294

European-Non Finnish (NFE) AF: 0.388 AC: 26343 AN: 67974

Other (OTH) AF: 0.344 AC: 728 AN: 2114

Alfa AF: 0.377 Hom.: 18680

Bravo AF: 0.361

Asia WGS AF: 0.446 AC: 1552 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.52
CADD	Benign	16
DANN	Benign	0.87
PhyloP100		0.088

Splicing

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

Other links and lift over

dbSNP: rs16976728; hg19: chr16-27381712;