rs3848459

Positions:

• chr17-52827683-C-T

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 0.0792 in 152,012 control chromosomes in the GnomAD database, including 1,121 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 0.079 (1121 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.212

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.221 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0789 AC: 11986 AN: 151894 Hom.: 1108 Cov.: 29

Gnomad AFR AF: 0.224

Gnomad AMI AF: 0.0198

Gnomad AMR AF: 0.0397

Gnomad ASJ AF: 0.0401

Gnomad EAS AF: 0.000387

Gnomad SAS AF: 0.0459

Gnomad FIN AF: 0.00311

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0235

Gnomad OTH AF: 0.0558

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

GnomAD4 genome AF: 0.0792 AC: 12032 AN: 152012 Hom.: 1121 Cov.: 29 AF XY: 0.0753 AC XY: 5599 AN XY: 74346

Gnomad4 AFR AF: 0.225

Gnomad4 AMR AF: 0.0396

Gnomad4 ASJ AF: 0.0401

Gnomad4 EAS AF: 0.000388

Gnomad4 SAS AF: 0.0453

Gnomad4 FIN AF: 0.00311

Gnomad4 NFE AF: 0.0235

Gnomad4 OTH AF: 0.0552

Alfa AF: 0.0614 Hom.: 132

Bravo AF: 0.0871

Asia WGS AF: 0.0400 AC: 144 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.1
DANN	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3848459; hg19: chr17-50905043;