rs836994

Variant names:

• chr16-54179629-C-T
• rs836994

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 0.62 in 151,224 control chromosomes in the GnomAD database, including 29,306 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 0.62 (29306 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.26

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.675 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: 0.620 AC: 93748 AN: 151108 Hom.: 29277 Cov.: 28

Gnomad AFR AF: 0.683

Gnomad AMI AF: 0.492

Gnomad AMR AF: 0.625

Gnomad ASJ AF: 0.603

Gnomad EAS AF: 0.481

Gnomad SAS AF: 0.594

Gnomad FIN AF: 0.578

Gnomad MID AF: 0.583

Gnomad NFE AF: 0.604

Gnomad OTH AF: 0.601

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

GnomAD4 genome AF: 0.620 AC: 93826 AN: 151224 Hom.: 29306 Cov.: 28 AF XY: 0.619 AC XY: 45730 AN XY: 73830

Gnomad4 AFR AF: 0.682

Gnomad4 AMR AF: 0.626

Gnomad4 ASJ AF: 0.603

Gnomad4 EAS AF: 0.481

Gnomad4 SAS AF: 0.592

Gnomad4 FIN AF: 0.578

Gnomad4 NFE AF: 0.604

Gnomad4 OTH AF: 0.604

Alfa AF: 0.608 Hom.: 15393

Bravo AF: 0.625

Asia WGS AF: 0.528 AC: 1835 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.012
DANN	Benign	0.20

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs836994; hg19: chr16-54213541;