rs4461066

Variant names:

• chr16-52877697-C-T
• rs4461066

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 0.413 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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.442 AC: 18307 AN: 41396

American (AMR) AF: 0.464 AC: 7089 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.344 AC: 1191 AN: 3466

East Asian (EAS) AF: 0.599 AC: 3075 AN: 5130

South Asian (SAS) AF: 0.406 AC: 1955 AN: 4820

European-Finnish (FIN) AF: 0.402 AC: 4242 AN: 10562

Middle Eastern (MID) AF: 0.299 AC: 88 AN: 294

European-Non Finnish (NFE) AF: 0.377 AC: 25626 AN: 67962

Other (OTH) AF: 0.403 AC: 851 AN: 2114

Alfa AF: 0.390 Hom.: 7040

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
PhyloP100		0.043

Splicing

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

Other links and lift over

dbSNP: rs4461066; hg19: chr16-52911609;