chr15-54829321-G-T

Variant names:

• chr15-54829321-G-T
• rs10518784

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 0.207 in 152,102 control chromosomes in the GnomAD database, including 3,470 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 0.21 (3470 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.244 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: 0.207 AC: 31402 AN: 151984 Hom.: 3465 Cov.: 32

Gnomad AFR AF: 0.163

Gnomad AMI AF: 0.333

Gnomad AMR AF: 0.201

Gnomad ASJ AF: 0.206

Gnomad EAS AF: 0.0444

Gnomad SAS AF: 0.188

Gnomad FIN AF: 0.201

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.247

Gnomad OTH AF: 0.205

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

GnomAD4 genome AF: 0.207 AC: 31427 AN: 152102 Hom.: 3470 Cov.: 32 AF XY: 0.203 AC XY: 15117 AN XY: 74372

African (AFR) AF: 0.163 AC: 6773 AN: 41510

American (AMR) AF: 0.201 AC: 3067 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.206 AC: 713 AN: 3466

East Asian (EAS) AF: 0.0447 AC: 231 AN: 5168

South Asian (SAS) AF: 0.188 AC: 908 AN: 4820

European-Finnish (FIN) AF: 0.201 AC: 2132 AN: 10588

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.247 AC: 16804 AN: 67956

Other (OTH) AF: 0.206 AC: 434 AN: 2110

Alfa AF: 0.231 Hom.: 18143

Bravo AF: 0.202

Asia WGS AF: 0.109 AC: 378 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.10
DANN	Benign	0.52
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs10518784; hg19: chr15-55121519;