rs964933

chr16-62314294-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 0.314 in 152,140 control chromosomes in the GnomAD database, including 7,801 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 (7801 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.441

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.369 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: 0.314 AC: 47744 AN: 152022 Hom.: 7793 Cov.: 33

Gnomad AFR AF: 0.237

Gnomad AMI AF: 0.253

Gnomad AMR AF: 0.377

Gnomad ASJ AF: 0.362

Gnomad EAS AF: 0.235

Gnomad SAS AF: 0.241

Gnomad FIN AF: 0.338

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.353

Gnomad OTH AF: 0.321

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

GnomAD4 genome AF: 0.314 AC: 47779 AN: 152140 Hom.: 7801 Cov.: 33 AF XY: 0.312 AC XY: 23174 AN XY: 74356

Gnomad4 AFR AF: 0.237

Gnomad4 AMR AF: 0.377

Gnomad4 ASJ AF: 0.362

Gnomad4 EAS AF: 0.236

Gnomad4 SAS AF: 0.243

Gnomad4 FIN AF: 0.338

Gnomad4 NFE AF: 0.353

Gnomad4 OTH AF: 0.317

Alfa AF: 0.328 Hom.: 1413

Bravo AF: 0.315

Asia WGS AF: 0.255 AC: 887 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.84
Dann	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs964933; hg19: chr16-62348198;