rs879606

chr17-39625596-A-G

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;