rs4461066

Variant names:

• chr16-52877697-C-T
• rs4461066

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 0.413 in 151,918 control chromosomes in the GnomAD database, including 13,114 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 0.41 (13114 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0430

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.582 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: 0.413 AC: 62679 AN: 151800 Hom.: 13092 Cov.: 32

Gnomad AFR AF: 0.442

Gnomad AMI AF: 0.336

Gnomad AMR AF: 0.465

Gnomad ASJ AF: 0.344

Gnomad EAS AF: 0.599

Gnomad SAS AF: 0.405

Gnomad FIN AF: 0.402

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.377

Gnomad OTH AF: 0.405

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

GnomAD4 genome AF: 0.413 AC: 62730 AN: 151918 Hom.: 13114 Cov.: 32 AF XY: 0.412 AC XY: 30596 AN XY: 74226

Gnomad4 AFR AF: 0.442

Gnomad4 AMR AF: 0.464

Gnomad4 ASJ AF: 0.344

Gnomad4 EAS AF: 0.599

Gnomad4 SAS AF: 0.406

Gnomad4 FIN AF: 0.402

Gnomad4 NFE AF: 0.377

Gnomad4 OTH AF: 0.403

Alfa AF: 0.389 Hom.: 5147

Bravo AF: 0.426

Asia WGS AF: 0.457 AC: 1587 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.0
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4461066; hg19: chr16-52911609;