rs7675998

Variant names:

• chr4-163086668-A-G
• rs7675998

Your query was ambiguous. Multiple possible variants found:

• chr4-163086668-A-G
• chr4-163086668-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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

Sep 01, 2016

Department of Orthopeadics and Traumatology, Nanfang Hospital

Significance: association

Review Status: no assertion criteria provided

Collection Method: case-control

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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;