rs878329

Variant names:

• chr17-5649930-G-C
• rs878329

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 0.438 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
• Publications: 28 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.425 AC: 17606 AN: 41378

American (AMR) AF: 0.461 AC: 7033 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.513 AC: 1779 AN: 3468

East Asian (EAS) AF: 0.182 AC: 936 AN: 5152

South Asian (SAS) AF: 0.425 AC: 2048 AN: 4824

European-Finnish (FIN) AF: 0.435 AC: 4577 AN: 10520

Middle Eastern (MID) AF: 0.497 AC: 145 AN: 292

European-Non Finnish (NFE) AF: 0.454 AC: 30880 AN: 67946

Other (OTH) AF: 0.444 AC: 935 AN: 2106

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
PhyloP100		1.6

Splicing

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

Other links and lift over

dbSNP: rs878329; hg19: chr17-5553250;