16-27310774-C-T

Variant names:

• chr16-27310774-C-T
• rs2057768

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 0.293 in 152,048 control chromosomes in the GnomAD database, including 6,720 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 0.29 (6720 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.01

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.512 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.294 AC: 44606 AN: 151930 Hom.: 6720 Cov.: 32

Gnomad AFR AF: 0.284

Gnomad AMI AF: 0.283

Gnomad AMR AF: 0.258

Gnomad ASJ AF: 0.215

Gnomad EAS AF: 0.529

Gnomad SAS AF: 0.369

Gnomad FIN AF: 0.252

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.295

Gnomad OTH AF: 0.301

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

GnomAD4 genome AF: 0.293 AC: 44626 AN: 152048 Hom.: 6720 Cov.: 32 AF XY: 0.292 AC XY: 21736 AN XY: 74314

Gnomad4 AFR AF: 0.284

Gnomad4 AMR AF: 0.258

Gnomad4 ASJ AF: 0.215

Gnomad4 EAS AF: 0.529

Gnomad4 SAS AF: 0.368

Gnomad4 FIN AF: 0.252

Gnomad4 NFE AF: 0.295

Gnomad4 OTH AF: 0.305

Alfa AF: 0.286 Hom.: 10098

Bravo AF: 0.293

Asia WGS AF: 0.415 AC: 1445 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	7.0
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2057768; hg19: chr16-27322095;