chr16-56961322-C-A

Variant names:

• chr16-56961322-C-A
• rs1800776

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 0.0573 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
• Publications: 15 publications found

ACMG classification

Our verdict: Benign. The variant received -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

GnomAD2 exomes AF: 0.0520 AC: 9140 AN: 175874 AF XY: 0.0526

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 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

African (AFR) AF: 0.0303 AC: 296 AN: 9770

American (AMR) AF: 0.0474 AC: 1489 AN: 31394

Ashkenazi Jewish (ASJ) AF: 0.0608 AC: 679 AN: 11170

East Asian (EAS) AF: 0.000337 AC: 4 AN: 11880

South Asian (SAS) AF: 0.0329 AC: 2028 AN: 61666

European-Finnish (FIN) AF: 0.0327 AC: 483 AN: 14778

Middle Eastern (MID) AF: 0.125 AC: 348 AN: 2788

European-Non Finnish (NFE) AF: 0.0757 AC: 13012 AN: 171854

Other (OTH) AF: 0.0673 AC: 1026 AN: 15252

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

African (AFR) AF: 0.0323 AC: 1343 AN: 41528

American (AMR) AF: 0.0549 AC: 839 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0611 AC: 212 AN: 3470

East Asian (EAS) AF: 0.000771 AC: 4 AN: 5186

South Asian (SAS) AF: 0.0316 AC: 152 AN: 4814

European-Finnish (FIN) AF: 0.0301 AC: 319 AN: 10604

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.0754 AC: 5130 AN: 68002

Other (OTH) AF: 0.0634 AC: 134 AN: 2112

Alfa AF: 0.0539 Hom.: 117

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
PhyloP100		-0.62

Splicing

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

Other links and lift over

dbSNP: rs1800776; hg19: chr16-56995234;