rs878329

Variant names:

• chr17-5649930-G-C
• rs878329

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 0.438 in 151,848 control chromosomes in the GnomAD database, including 14,816 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 0.44 (14816 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.59

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.452 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: 0.438 AC: 66420 AN: 151730 Hom.: 14794 Cov.: 31

Gnomad AFR AF: 0.425

Gnomad AMI AF: 0.616

Gnomad AMR AF: 0.461

Gnomad ASJ AF: 0.513

Gnomad EAS AF: 0.181

Gnomad SAS AF: 0.423

Gnomad FIN AF: 0.435

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.454

Gnomad OTH AF: 0.439

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

GnomAD4 genome AF: 0.438 AC: 66498 AN: 151848 Hom.: 14816 Cov.: 31 AF XY: 0.438 AC XY: 32491 AN XY: 74214

Gnomad4 AFR AF: 0.425

Gnomad4 AMR AF: 0.461

Gnomad4 ASJ AF: 0.513

Gnomad4 EAS AF: 0.182

Gnomad4 SAS AF: 0.425

Gnomad4 FIN AF: 0.435

Gnomad4 NFE AF: 0.454

Gnomad4 OTH AF: 0.444

Alfa AF: 0.446 Hom.: 1892

Bravo AF: 0.438

Asia WGS AF: 0.352 AC: 1224 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.5
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs878329; hg19: chr17-5553250;