16-27312083-C-T

Variant names:

• chr16-27312083-C-T
• rs2107356

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 0.352 in 152,038 control chromosomes in the GnomAD database, including 10,509 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 0.35 (10509 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0870
• Publications: 30 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.41 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: 0.353 AC: 53590 AN: 151920 Hom.: 10518 Cov.: 32

Gnomad AFR AF: 0.180

Gnomad AMI AF: 0.538

Gnomad AMR AF: 0.405

Gnomad ASJ AF: 0.448

Gnomad EAS AF: 0.371

Gnomad SAS AF: 0.384

Gnomad FIN AF: 0.476

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.415

Gnomad OTH AF: 0.387

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

GnomAD4 genome AF: 0.352 AC: 53576 AN: 152038 Hom.: 10509 Cov.: 32 AF XY: 0.357 AC XY: 26570 AN XY: 74332

African (AFR) AF: 0.180 AC: 7443 AN: 41460

American (AMR) AF: 0.405 AC: 6187 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.448 AC: 1553 AN: 3466

East Asian (EAS) AF: 0.371 AC: 1921 AN: 5172

South Asian (SAS) AF: 0.383 AC: 1846 AN: 4818

European-Finnish (FIN) AF: 0.476 AC: 5029 AN: 10558

Middle Eastern (MID) AF: 0.408 AC: 120 AN: 294

European-Non Finnish (NFE) AF: 0.414 AC: 28171 AN: 67964

Other (OTH) AF: 0.386 AC: 815 AN: 2112

Alfa AF: 0.371 Hom.: 6743

Bravo AF: 0.342

Asia WGS AF: 0.355 AC: 1234 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.5
DANN	Benign	0.31
PhyloP100		-0.087

Splicing

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

Other links and lift over

dbSNP: rs2107356; hg19: chr16-27323404;