16-2830104-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 0.691 in 644,222 control chromosomes in the GnomAD database, including 154,467 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 0.71 (38617 hom., cov: 35)
  • Exomes 𝑓: 0.68 (115850 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.687

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 (AFR) allele frequency at 95% confidence interval = 0.776 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: 0.710 AC: 107999 AN: 152082 Hom.: 38591 Cov.: 35

Gnomad AFR AF: 0.784

Gnomad AMI AF: 0.711

Gnomad AMR AF: 0.668

Gnomad ASJ AF: 0.740

Gnomad EAS AF: 0.668

Gnomad SAS AF: 0.690

Gnomad FIN AF: 0.628

Gnomad MID AF: 0.747

Gnomad NFE AF: 0.690

Gnomad OTH AF: 0.729

GnomAD4 exome AF: 0.685 AC: 336909 AN: 492022 Hom.: 115850 AF XY: 0.686 AC XY: 174832 AN XY: 254712

Gnomad4 AFR exome AF: 0.776

Gnomad4 AMR exome AF: 0.643

Gnomad4 ASJ exome AF: 0.728

Gnomad4 EAS exome AF: 0.607

Gnomad4 SAS exome AF: 0.704

Gnomad4 FIN exome AF: 0.641

Gnomad4 NFE exome AF: 0.690

Gnomad4 OTH exome AF: 0.699

GnomAD4 genome AF: 0.710 AC: 108081 AN: 152200 Hom.: 38617 Cov.: 35 AF XY: 0.705 AC XY: 52442 AN XY: 74424

Gnomad4 AFR AF: 0.783

Gnomad4 AMR AF: 0.669

Gnomad4 ASJ AF: 0.740

Gnomad4 EAS AF: 0.668

Gnomad4 SAS AF: 0.691

Gnomad4 FIN AF: 0.628

Gnomad4 NFE AF: 0.690

Gnomad4 OTH AF: 0.728

Alfa AF: 0.691 Hom.: 33687

Bravo AF: 0.713

Asia WGS AF: 0.664 AC: 2310 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	12
Dann	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9925556; hg19: chr16-2880105;