rs1800776

Variant names:

• chr16-56961322-C-A
• rs1800776

Your query was ambiguous. Multiple possible variants found:

• chr16-56961322-C-A
• chr16-56961322-C-G
• chr16-56961322-C-T

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;