rs17238405

Variant names:

• chr15-55798411-C-T
• rs17238405

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 0.298 in 151,996 control chromosomes in the GnomAD database, including 6,926 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 0.30 (6926 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.680
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.311 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: 0.298 AC: 45281 AN: 151878 Hom.: 6918 Cov.: 32

Gnomad AFR AF: 0.294

Gnomad AMI AF: 0.388

Gnomad AMR AF: 0.232

Gnomad ASJ AF: 0.250

Gnomad EAS AF: 0.203

Gnomad SAS AF: 0.230

Gnomad FIN AF: 0.396

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.315

Gnomad OTH AF: 0.274

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

GnomAD4 genome AF: 0.298 AC: 45312 AN: 151996 Hom.: 6926 Cov.: 32 AF XY: 0.297 AC XY: 22085 AN XY: 74258

African (AFR) AF: 0.294 AC: 12182 AN: 41476

American (AMR) AF: 0.232 AC: 3541 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.250 AC: 867 AN: 3468

East Asian (EAS) AF: 0.204 AC: 1052 AN: 5164

South Asian (SAS) AF: 0.230 AC: 1109 AN: 4820

European-Finnish (FIN) AF: 0.396 AC: 4174 AN: 10532

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.315 AC: 21395 AN: 67964

Other (OTH) AF: 0.278 AC: 584 AN: 2104

Alfa AF: 0.295 Hom.: 2114

Bravo AF: 0.289

Asia WGS AF: 0.247 AC: 858 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	13
DANN	Benign	0.55
PhyloP100		0.68

Splicing

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

Other links and lift over

dbSNP: rs17238405; hg19: chr15-56090609;