rs879606

Variant names:

• chr17-39625596-A-G
• rs879606

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 0.728 in 151,996 control chromosomes in the GnomAD database, including 41,352 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 0.73 (41352 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.03

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.819 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: 0.728 AC: 110570 AN: 151878 Hom.: 41325 Cov.: 32

Gnomad AFR AF: 0.578

Gnomad AMI AF: 0.840

Gnomad AMR AF: 0.692

Gnomad ASJ AF: 0.841

Gnomad EAS AF: 0.445

Gnomad SAS AF: 0.764

Gnomad FIN AF: 0.814

Gnomad MID AF: 0.785

Gnomad NFE AF: 0.825

Gnomad OTH AF: 0.749

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

GnomAD4 genome AF: 0.728 AC: 110661 AN: 151996 Hom.: 41352 Cov.: 32 AF XY: 0.725 AC XY: 53812 AN XY: 74274

Gnomad4 AFR AF: 0.578

Gnomad4 AMR AF: 0.692

Gnomad4 ASJ AF: 0.841

Gnomad4 EAS AF: 0.445

Gnomad4 SAS AF: 0.764

Gnomad4 FIN AF: 0.814

Gnomad4 NFE AF: 0.825

Gnomad4 OTH AF: 0.749

Alfa AF: 0.812 Hom.: 66456

Bravo AF: 0.711

Asia WGS AF: 0.668 AC: 2325 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.1
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs879606; hg19: chr17-37781849;