rs2055858

Positions:

• chr15-45022070-G-C
• chr15-45022070-G-T

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 0.194 in 151,526 control chromosomes in the GnomAD database, including 3,406 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 0.19 (3406 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.88

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.07).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.305 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.194 AC: 29382 AN: 151408 Hom.: 3388 Cov.: 31

Gnomad AFR AF: 0.305

Gnomad AMI AF: 0.173

Gnomad AMR AF: 0.204

Gnomad ASJ AF: 0.0713

Gnomad EAS AF: 0.317

Gnomad SAS AF: 0.214

Gnomad FIN AF: 0.191

Gnomad MID AF: 0.0987

Gnomad NFE AF: 0.122

Gnomad OTH AF: 0.178

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

GnomAD4 genome AF: 0.194 AC: 29449 AN: 151526 Hom.: 3406 Cov.: 31 AF XY: 0.197 AC XY: 14593 AN XY: 74022

Gnomad4 AFR AF: 0.305

Gnomad4 AMR AF: 0.205

Gnomad4 ASJ AF: 0.0713

Gnomad4 EAS AF: 0.318

Gnomad4 SAS AF: 0.215

Gnomad4 FIN AF: 0.191

Gnomad4 NFE AF: 0.122

Gnomad4 OTH AF: 0.187

Alfa AF: 0.162 Hom.: 300

Bravo AF: 0.202

Asia WGS AF: 0.298 AC: 1036 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.58
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2055858; hg19: chr15-45314268;