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. The variant received -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
• Publications: 78 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.797 AC: 33112 AN: 41526

American (AMR) AF: 0.793 AC: 12123 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.762 AC: 2645 AN: 3472

East Asian (EAS) AF: 0.826 AC: 4272 AN: 5174

South Asian (SAS) AF: 0.835 AC: 4029 AN: 4824

European-Finnish (FIN) AF: 0.811 AC: 8584 AN: 10580

Middle Eastern (MID) AF: 0.677 AC: 199 AN: 294

European-Non Finnish (NFE) AF: 0.776 AC: 52790 AN: 68002

Other (OTH) AF: 0.768 AC: 1620 AN: 2110

Alfa AF: 0.783 Hom.: 60411

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
PhyloP100		-0.069

Splicing

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

Other links and lift over

dbSNP: rs7675998; hg19: chr4-164007820;