rs17486446

Variant names:

• chr15-49848931-A-G
• rs17486446

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.184 in 152,172 control chromosomes in the GnomAD database, including 3,254 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 0.18 (3254 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0280

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.262 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: 0.184 AC: 27966 AN: 152054 Hom.: 3255 Cov.: 32

Gnomad AFR AF: 0.0517

Gnomad AMI AF: 0.371

Gnomad AMR AF: 0.181

Gnomad ASJ AF: 0.232

Gnomad EAS AF: 0.0241

Gnomad SAS AF: 0.161

Gnomad FIN AF: 0.234

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.266

Gnomad OTH AF: 0.207

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

GnomAD4 genome AF: 0.184 AC: 27956 AN: 152172 Hom.: 3254 Cov.: 32 AF XY: 0.180 AC XY: 13422 AN XY: 74384

Gnomad4 AFR AF: 0.0515

Gnomad4 AMR AF: 0.180

Gnomad4 ASJ AF: 0.232

Gnomad4 EAS AF: 0.0241

Gnomad4 SAS AF: 0.162

Gnomad4 FIN AF: 0.234

Gnomad4 NFE AF: 0.266

Gnomad4 OTH AF: 0.205

Alfa AF: 0.217 Hom.: 648

Bravo AF: 0.172

Asia WGS AF: 0.0770 AC: 268 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	3.6
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17486446; hg19: chr15-50141128;