rs1800776

chr16-56961322-C-A

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 0.0573 in 482,760 control chromosomes in the GnomAD database, including 1,005 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 0.055 (274 hom., cov: 33)
  • Exomes 𝑓: 0.059 (731 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.620

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0737 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0547 AC: 8313 AN: 152090 Hom.: 273 Cov.: 33

Gnomad AFR AF: 0.0324

Gnomad AMI AF: 0.140

Gnomad AMR AF: 0.0551

Gnomad ASJ AF: 0.0611

Gnomad EAS AF: 0.000770

Gnomad SAS AF: 0.0315

Gnomad FIN AF: 0.0301

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.0754

Gnomad OTH AF: 0.0646

GnomAD3 exomes AF: 0.0520 AC: 9140 AN: 175874 Hom.: 299 AF XY: 0.0526 AC XY: 5058 AN XY: 96146

Gnomad AFR exome AF: 0.0287

Gnomad AMR exome AF: 0.0463

Gnomad ASJ exome AF: 0.0588

Gnomad EAS exome AF: 0.000414

Gnomad SAS exome AF: 0.0335

Gnomad FIN exome AF: 0.0294

Gnomad NFE exome AF: 0.0735

Gnomad OTH exome AF: 0.0724

GnomAD4 exome AF: 0.0586 AC: 19365 AN: 330552 Hom.: 731 Cov.: 0 AF XY: 0.0575 AC XY: 10853 AN XY: 188680

Gnomad4 AFR exome AF: 0.0303

Gnomad4 AMR exome AF: 0.0474

Gnomad4 ASJ exome AF: 0.0608

Gnomad4 EAS exome AF: 0.000337

Gnomad4 SAS exome AF: 0.0329

Gnomad4 FIN exome AF: 0.0327

Gnomad4 NFE exome AF: 0.0757

Gnomad4 OTH exome AF: 0.0673

GnomAD4 genome AF: 0.0546 AC: 8313 AN: 152208 Hom.: 274 Cov.: 33 AF XY: 0.0519 AC XY: 3865 AN XY: 74418

Gnomad4 AFR AF: 0.0323

Gnomad4 AMR AF: 0.0549

Gnomad4 ASJ AF: 0.0611

Gnomad4 EAS AF: 0.000771

Gnomad4 SAS AF: 0.0316

Gnomad4 FIN AF: 0.0301

Gnomad4 NFE AF: 0.0754

Gnomad4 OTH AF: 0.0634

Alfa AF: 0.0619 Hom.: 65

Bravo AF: 0.0571

Asia WGS AF: 0.0190 AC: 66 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	1.2
Dann	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1800776; hg19: chr16-56995234;