rs2192859

Variant names:

• chr16-52880837-C-T
• rs2192859

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 0.352 in 152,088 control chromosomes in the GnomAD database, including 9,905 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 0.35 (9905 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.702
• Publications: 8 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.58 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: 0.352 AC: 53439 AN: 151970 Hom.: 9898 Cov.: 33

Gnomad AFR AF: 0.229

Gnomad AMI AF: 0.336

Gnomad AMR AF: 0.440

Gnomad ASJ AF: 0.344

Gnomad EAS AF: 0.597

Gnomad SAS AF: 0.404

Gnomad FIN AF: 0.404

Gnomad MID AF: 0.296

Gnomad NFE AF: 0.377

Gnomad OTH AF: 0.360

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

GnomAD4 genome AF: 0.352 AC: 53465 AN: 152088 Hom.: 9905 Cov.: 33 AF XY: 0.353 AC XY: 26263 AN XY: 74342

African (AFR) AF: 0.229 AC: 9502 AN: 41490

American (AMR) AF: 0.440 AC: 6721 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.344 AC: 1192 AN: 3470

East Asian (EAS) AF: 0.597 AC: 3089 AN: 5170

South Asian (SAS) AF: 0.405 AC: 1951 AN: 4820

European-Finnish (FIN) AF: 0.404 AC: 4265 AN: 10570

Middle Eastern (MID) AF: 0.291 AC: 85 AN: 292

European-Non Finnish (NFE) AF: 0.377 AC: 25599 AN: 67982

Other (OTH) AF: 0.357 AC: 755 AN: 2112

Alfa AF: 0.379 Hom.: 1884

Bravo AF: 0.356

Asia WGS AF: 0.441 AC: 1530 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	11
DANN	Benign	0.73
PhyloP100		0.70

Splicing

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

Other links and lift over

dbSNP: rs2192859; hg19: chr16-52914749;