chr16-51865966-C-T

Variant names:

• chr16-51865966-C-T
• rs1110494

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 0.315 in 152,070 control chromosomes in the GnomAD database, including 7,765 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 0.31 (7765 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.287

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.4 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: 0.315 AC: 47827 AN: 151950 Hom.: 7756 Cov.: 33

Gnomad AFR AF: 0.250

Gnomad AMI AF: 0.265

Gnomad AMR AF: 0.408

Gnomad ASJ AF: 0.374

Gnomad EAS AF: 0.392

Gnomad SAS AF: 0.369

Gnomad FIN AF: 0.278

Gnomad MID AF: 0.366

Gnomad NFE AF: 0.326

Gnomad OTH AF: 0.331

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

GnomAD4 genome AF: 0.315 AC: 47876 AN: 152070 Hom.: 7765 Cov.: 33 AF XY: 0.315 AC XY: 23428 AN XY: 74342

Gnomad4 AFR AF: 0.250

Gnomad4 AMR AF: 0.408

Gnomad4 ASJ AF: 0.374

Gnomad4 EAS AF: 0.393

Gnomad4 SAS AF: 0.370

Gnomad4 FIN AF: 0.278

Gnomad4 NFE AF: 0.326

Gnomad4 OTH AF: 0.332

Alfa AF: 0.311 Hom.: 890

Bravo AF: 0.320

Asia WGS AF: 0.341 AC: 1189 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.3
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1110494; hg19: chr16-51899877;