rs2045112

Variant names:

• chr15-99762767-C-T
• rs2045112

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 0.285 in 152,074 control chromosomes in the GnomAD database, including 6,413 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 0.29 (6413 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.280
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.399 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: 0.285 AC: 43324 AN: 151956 Hom.: 6398 Cov.: 33

Gnomad AFR AF: 0.249

Gnomad AMI AF: 0.272

Gnomad AMR AF: 0.406

Gnomad ASJ AF: 0.354

Gnomad EAS AF: 0.377

Gnomad SAS AF: 0.327

Gnomad FIN AF: 0.283

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.266

Gnomad OTH AF: 0.310

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

GnomAD4 genome AF: 0.285 AC: 43368 AN: 152074 Hom.: 6413 Cov.: 33 AF XY: 0.290 AC XY: 21541 AN XY: 74358

African (AFR) AF: 0.249 AC: 10320 AN: 41470

American (AMR) AF: 0.408 AC: 6233 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.354 AC: 1230 AN: 3470

East Asian (EAS) AF: 0.378 AC: 1948 AN: 5158

South Asian (SAS) AF: 0.327 AC: 1574 AN: 4820

European-Finnish (FIN) AF: 0.283 AC: 2995 AN: 10578

Middle Eastern (MID) AF: 0.255 AC: 75 AN: 294

European-Non Finnish (NFE) AF: 0.266 AC: 18093 AN: 67970

Other (OTH) AF: 0.309 AC: 652 AN: 2110

Alfa AF: 0.279 Hom.: 16309

Bravo AF: 0.297

Asia WGS AF: 0.341 AC: 1186 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.59
DANN	Benign	0.32
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs2045112; hg19: chr15-100302972;