rs17176829

Positions:

• chr3-103124186-G-A

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 0.337 in 151,780 control chromosomes in the GnomAD database, including 8,686 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 0.34 (8686 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.16

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.419 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.337 AC: 51077 AN: 151668 Hom.: 8678 Cov.: 32

Gnomad AFR AF: 0.312

Gnomad AMI AF: 0.295

Gnomad AMR AF: 0.376

Gnomad ASJ AF: 0.318

Gnomad EAS AF: 0.433

Gnomad SAS AF: 0.294

Gnomad FIN AF: 0.288

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.348

Gnomad OTH AF: 0.328

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

GnomAD4 genome AF: 0.337 AC: 51115 AN: 151780 Hom.: 8686 Cov.: 32 AF XY: 0.336 AC XY: 24904 AN XY: 74164

Gnomad4 AFR AF: 0.313

Gnomad4 AMR AF: 0.375

Gnomad4 ASJ AF: 0.318

Gnomad4 EAS AF: 0.434

Gnomad4 SAS AF: 0.293

Gnomad4 FIN AF: 0.288

Gnomad4 NFE AF: 0.348

Gnomad4 OTH AF: 0.328

Alfa AF: 0.329 Hom.: 1240

Bravo AF: 0.343

Asia WGS AF: 0.360 AC: 1245 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.0040
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17176829; hg19: chr3-102843030;