rs2215502

Variant names:

• chr18-28204055-T-C
• rs2215502

Your query was ambiguous. Multiple possible variants found:

• chr18-28204055-T-C
• chr18-28204055-T-G

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 0.579 in 152,068 control chromosomes in the GnomAD database, including 27,446 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 0.58 (27446 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.09
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.692 is higher than 0.05.

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: 0.580 AC: 88064 AN: 151948 Hom.: 27444 Cov.: 33

Gnomad AFR AF: 0.324

Gnomad AMI AF: 0.766

Gnomad AMR AF: 0.662

Gnomad ASJ AF: 0.748

Gnomad EAS AF: 0.712

Gnomad SAS AF: 0.668

Gnomad FIN AF: 0.609

Gnomad MID AF: 0.718

Gnomad NFE AF: 0.682

Gnomad OTH AF: 0.644

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

GnomAD4 genome AF: 0.579 AC: 88103 AN: 152068 Hom.: 27446 Cov.: 33 AF XY: 0.581 AC XY: 43210 AN XY: 74330

African (AFR) AF: 0.325 AC: 13465 AN: 41488

American (AMR) AF: 0.661 AC: 10100 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.748 AC: 2593 AN: 3468

East Asian (EAS) AF: 0.711 AC: 3678 AN: 5170

South Asian (SAS) AF: 0.669 AC: 3227 AN: 4824

European-Finnish (FIN) AF: 0.609 AC: 6433 AN: 10562

Middle Eastern (MID) AF: 0.704 AC: 207 AN: 294

European-Non Finnish (NFE) AF: 0.682 AC: 46346 AN: 67970

Other (OTH) AF: 0.643 AC: 1357 AN: 2110

Alfa AF: 0.653 Hom.: 41297

Bravo AF: 0.574

Asia WGS AF: 0.644 AC: 2242 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.7
DANN	Benign	0.70
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs2215502; hg19: chr18-25784019;