rs1115333

Variant names:

• chr15-55055255-A-G
• rs1115333

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0267 in 152,146 control chromosomes in the GnomAD database, including 76 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 0.027 (76 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.332
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BS1: Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.0267 (4056/152146) while in subpopulation AFR AF = 0.0339 (1409/41526). AF 95% confidence interval is 0.0325. There are 76 homozygotes in GnomAd4. There are 2030 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 76 gene

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.0266 AC: 4047 AN: 152028 Hom.: 76 Cov.: 32

Gnomad AFR AF: 0.0339

Gnomad AMI AF: 0.123

Gnomad AMR AF: 0.0226

Gnomad ASJ AF: 0.0193

Gnomad EAS AF: 0.0221

Gnomad SAS AF: 0.0184

Gnomad FIN AF: 0.0346

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.0220

Gnomad OTH AF: 0.0254

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

GnomAD4 genome AF: 0.0267 AC: 4056 AN: 152146 Hom.: 76 Cov.: 32 AF XY: 0.0273 AC XY: 2030 AN XY: 74402

African (AFR) AF: 0.0339 AC: 1409 AN: 41526

American (AMR) AF: 0.0225 AC: 343 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.0193 AC: 67 AN: 3468

East Asian (EAS) AF: 0.0222 AC: 115 AN: 5188

South Asian (SAS) AF: 0.0187 AC: 90 AN: 4824

European-Finnish (FIN) AF: 0.0346 AC: 367 AN: 10600

Middle Eastern (MID) AF: 0.00340 AC: 1 AN: 294

European-Non Finnish (NFE) AF: 0.0220 AC: 1495 AN: 67958

Other (OTH) AF: 0.0270 AC: 57 AN: 2112

Alfa AF: 0.0231 Hom.: 11

Bravo AF: 0.0264

Asia WGS AF: 0.0480 AC: 166 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.17
DANN	Benign	0.69
PhyloP100		-0.33

Splicing

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

Other links and lift over

dbSNP: rs1115333; hg19: chr15-55347453;