rs2055858

Variant names:

• chr15-45022070-G-C
• rs2055858

Your query was ambiguous. Multiple possible variants found:

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

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 0.194 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
• Publications: 8 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.305 AC: 12587 AN: 41242

American (AMR) AF: 0.205 AC: 3121 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.0713 AC: 247 AN: 3466

East Asian (EAS) AF: 0.318 AC: 1628 AN: 5126

South Asian (SAS) AF: 0.215 AC: 1030 AN: 4788

European-Finnish (FIN) AF: 0.191 AC: 1996 AN: 10458

Middle Eastern (MID) AF: 0.0993 AC: 29 AN: 292

European-Non Finnish (NFE) AF: 0.122 AC: 8259 AN: 67904

Other (OTH) AF: 0.187 AC: 395 AN: 2108

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
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs2055858; hg19: chr15-45314268;