rs7675998

chr4-163086668-A-Gchr4-163086668-A-T

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 0.788 in 152,182 control chromosomes in the GnomAD database, including 47,310 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as association (no stars).

• Frequency: Genomes: 𝑓 0.79 (47310 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: association no assertion criteria provided O:1
• Conservation: PhyloP100: -0.0690

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.814 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: 0.788 AC: 119848 AN: 152064 Hom.: 47281 Cov.: 34

Gnomad AFR AF: 0.798

Gnomad AMI AF: 0.614

Gnomad AMR AF: 0.793

Gnomad ASJ AF: 0.762

Gnomad EAS AF: 0.825

Gnomad SAS AF: 0.835

Gnomad FIN AF: 0.811

Gnomad MID AF: 0.677

Gnomad NFE AF: 0.776

Gnomad OTH AF: 0.768

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

GnomAD4 genome AF: 0.788 AC: 119934 AN: 152182 Hom.: 47310 Cov.: 34 AF XY: 0.790 AC XY: 58793 AN XY: 74390

Gnomad4 AFR AF: 0.797

Gnomad4 AMR AF: 0.793

Gnomad4 ASJ AF: 0.762

Gnomad4 EAS AF: 0.826

Gnomad4 SAS AF: 0.835

Gnomad4 FIN AF: 0.811

Gnomad4 NFE AF: 0.776

Gnomad4 OTH AF: 0.768

Alfa AF: 0.724 Hom.: 2427

Bravo AF: 0.785

ClinVar

Significance: association

Submissions summary: Other:1

Revision: no assertion criteria provided

Submissions by phenotype

Chronic osteomyelitis Other:1

association, no assertion criteria provided

case-control

Department of Orthopeadics and Traumatology, Nanfang Hospital

Sep 01, 2016

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	3.0
Dann	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7675998; hg19: chr4-164007820;